diff --git a/.changeset/quiet-snakes-buy.md b/.changeset/quiet-snakes-buy.md
new file mode 100644
index 0000000000..9e26110fd3
--- /dev/null
+++ b/.changeset/quiet-snakes-buy.md
@@ -0,0 +1,8 @@
+---
+"@redocly/openapi-core": patch
+"@redocly/cli": patch
+---
+
+Fixed an issue where `--component-renaming-conflicts-severity` ignored conflicts when different files had components with the same name but different content.
+
+**Warning:** Autogenrated component names and `$ref` paths in bundled documents may differ from older releases.
diff --git a/packages/core/src/__tests__/__snapshots__/bundle-oas.test.ts.snap b/packages/core/src/__tests__/__snapshots__/bundle-oas.test.ts.snap
index 56cad3ec3d..a57b3da45e 100644
--- a/packages/core/src/__tests__/__snapshots__/bundle-oas.test.ts.snap
+++ b/packages/core/src/__tests__/__snapshots__/bundle-oas.test.ts.snap
@@ -26,7 +26,7 @@ components:
         $ref: '#/components/schemas/schema-a'
       examples:
         first:
-          $ref: '#/components/examples/param-a-first'
+          $ref: '#/components/examples/first-2'
         second:
           $ref: '#/components/examples/second'
     path-param:
@@ -41,7 +41,7 @@ components:
   examples:
     first:
       value: b1
-    param-a-first:
+    first-2:
       value: a1
     second:
       value: a2
diff --git a/packages/core/src/__tests__/__snapshots__/bundle.test.ts.snap b/packages/core/src/__tests__/__snapshots__/bundle.test.ts.snap
index 92d77e2686..a861b60211 100644
--- a/packages/core/src/__tests__/__snapshots__/bundle.test.ts.snap
+++ b/packages/core/src/__tests__/__snapshots__/bundle.test.ts.snap
@@ -1,5 +1,28 @@
 // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
+exports[`bundle > should bundle external pointer refs and warn for conflicting names 1`] = `
+openapi: 3.1.0
+paths:
+  /foo:
+    put:
+      parameters:
+        - $ref: '#/components/parameters/User-2'
+    get:
+      parameters:
+        - $ref: '#/components/parameters/User'
+components:
+  parameters:
+    User:
+      name: test
+      in: query
+      description: test-B
+    User-2:
+      name: test
+      in: path
+      description: test-A
+
+`;
+
 exports[`bundle > should bundle external refs 1`] = `
 openapi: 3.0.0
 paths:
@@ -26,7 +49,7 @@ components:
         $ref: '#/components/schemas/schema-a'
       examples:
         first:
-          $ref: '#/components/examples/param-a-first'
+          $ref: '#/components/examples/first-2'
         second:
           $ref: '#/components/examples/second'
     path-param:
@@ -41,7 +64,7 @@ components:
   examples:
     first:
       value: b1
-    param-a-first:
+    first-2:
       value: a1
     second:
       value: a2
@@ -124,6 +147,51 @@ components:
 
 `;
 
+exports[`bundle > should keep dotted JSON pointer schema keys and rename conflicting User schemas 1`] = `
+openapi: 3.0.0
+info:
+  title: Test ref with dots in component names
+  version: '1.0'
+  description: Demo
+  license:
+    name: DEMO
+    url: https://demo.com
+servers:
+  - url: http://demo.com/api
+paths:
+  /org-user:
+    get:
+      responses:
+        '200':
+          description: ok
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/my.org.User'
+    post:
+      responses:
+        '200':
+          description: ok
+          content:
+            application/json:
+              schema:
+                additionalProperties:
+                  $ref: '#/components/schemas/my.User'
+components:
+  schemas:
+    my.org.User:
+      type: object
+      properties:
+        orgId:
+          type: string
+    my.User:
+      type: object
+      properties:
+        displayName:
+          type: string
+
+`;
+
 exports[`bundle > should normalize self-file explicit $ref in nested referenced file 1`] = `
 openapi: 3.0.0
 info:
diff --git a/packages/core/src/__tests__/bundle-oas.test.ts b/packages/core/src/__tests__/bundle-oas.test.ts
index 0beba237b7..70d6ba7c41 100644
--- a/packages/core/src/__tests__/bundle-oas.test.ts
+++ b/packages/core/src/__tests__/bundle-oas.test.ts
@@ -47,7 +47,11 @@ describe('bundle-oas', () => {
       config: await createEmptyRedoclyConfig({}),
       ref: path.join(__dirname, 'fixtures/refs/openapi-with-external-refs.yaml'),
     });
-    expect(problems).toHaveLength(0);
+    expect(problems).toHaveLength(1);
+    expect(problems[0].severity).toBe('warn');
+    expect(problems[0].message).toEqual(
+      `Two schemas are referenced with the same name but different content. Renamed first to first-2.`
+    );
     expect(res.parsed).toMatchSnapshot();
   });
 
diff --git a/packages/core/src/__tests__/bundle.test.ts b/packages/core/src/__tests__/bundle.test.ts
index c9a88868a9..7da48ba2da 100644
--- a/packages/core/src/__tests__/bundle.test.ts
+++ b/packages/core/src/__tests__/bundle.test.ts
@@ -64,7 +64,11 @@ describe('bundle', () => {
       config: await createConfig({}),
       ref: path.join(__dirname, 'fixtures/refs/openapi-with-external-refs.yaml'),
     });
-    expect(problems).toHaveLength(0);
+    expect(problems).toHaveLength(1);
+    expect(problems[0].severity).toBe('warn');
+    expect(problems[0].message).toEqual(
+      `Two schemas are referenced with the same name but different content. Renamed first to first-2.`
+    );
     expect(res.parsed).toMatchSnapshot();
   });
 
@@ -119,6 +123,67 @@ describe('bundle', () => {
     );
   });
 
+  it('should bundle external pointer refs and warn for conflicting names', async () => {
+    const { bundle: res, problems } = await bundle({
+      config: await createConfig({}),
+      ref: path.join(
+        __dirname,
+        'fixtures/refs/openapi-with-external-refs-pointer-conflicting-names.yaml'
+      ),
+    });
+    expect(problems).toHaveLength(1);
+    expect(problems[0].severity).toBe('warn');
+    expect(problems[0].message).toEqual(
+      `Two schemas are referenced with the same name but different content. Renamed User to User-2.`
+    );
+    expect(res.parsed).toMatchSnapshot();
+  });
+
+  it('should bundle external pointer refs and do not show warnings for conflicting names', async () => {
+    const { problems } = await bundle({
+      config: await createConfig({}),
+      ref: path.join(
+        __dirname,
+        'fixtures/refs/openapi-with-external-refs-pointer-conflicting-names.yaml'
+      ),
+      componentRenamingConflicts: 'off',
+    });
+    expect(problems).toHaveLength(0);
+  });
+
+  it('should report error-severity problems for conflicting pointer ref names', async () => {
+    const { problems } = await bundle({
+      config: await createConfig({}),
+      ref: path.join(
+        __dirname,
+        'fixtures/refs/openapi-with-external-refs-pointer-conflicting-names.yaml'
+      ),
+      componentRenamingConflicts: 'error',
+    });
+    expect(problems).toHaveLength(1);
+    expect(problems[0].severity).toBe('error');
+    expect(problems[0].message).toEqual(
+      `Two schemas are referenced with the same name but different content. Renamed User to User-2.`
+    );
+  });
+
+  it('should keep dotted JSON pointer schema keys and rename conflicting User schemas', async () => {
+    const { bundle: res, problems } = await bundle({
+      config: await createConfig({}),
+      ref: path.join(
+        __dirname,
+        'fixtures/refs/openapi-bundle-external-schema-names-and-user-conflict.yaml'
+      ),
+    });
+
+    expect(problems).toHaveLength(0);
+    const schemas = (res.parsed as { components: { schemas: Record<string, unknown> } }).components
+      .schemas;
+    expect(schemas['my.org.User']).toBeDefined();
+    expect(schemas['my.User']).toBeDefined();
+    expect(res.parsed).toMatchSnapshot();
+  });
+
   it('should dereferenced correctly when used with dereference', async () => {
     const { bundle: res, problems } = await bundleDocument({
       externalRefResolver: new BaseResolver(),
diff --git a/packages/core/src/__tests__/fixtures/refs/component-a.yaml b/packages/core/src/__tests__/fixtures/refs/component-a.yaml
new file mode 100644
index 0000000000..7a151d3d71
--- /dev/null
+++ b/packages/core/src/__tests__/fixtures/refs/component-a.yaml
@@ -0,0 +1,6 @@
+components:
+  parameters:
+    User:
+      name: test
+      in: path
+      description: test-A
diff --git a/packages/core/src/__tests__/fixtures/refs/component-b.yaml b/packages/core/src/__tests__/fixtures/refs/component-b.yaml
new file mode 100644
index 0000000000..4c1323f61a
--- /dev/null
+++ b/packages/core/src/__tests__/fixtures/refs/component-b.yaml
@@ -0,0 +1,6 @@
+components:
+  parameters:
+    User:
+      name: test
+      in: query
+      description: test-B
diff --git a/packages/core/src/__tests__/fixtures/refs/external-ref-with-dots.yaml b/packages/core/src/__tests__/fixtures/refs/external-ref-with-dots.yaml
new file mode 100644
index 0000000000..838d9fa666
--- /dev/null
+++ b/packages/core/src/__tests__/fixtures/refs/external-ref-with-dots.yaml
@@ -0,0 +1,12 @@
+components:
+  schemas:
+    my.org.User:
+      type: object
+      properties:
+        orgId:
+          type: string
+    my.User:
+      type: object
+      properties:
+        displayName:
+          type: string
diff --git a/packages/core/src/__tests__/fixtures/refs/openapi-bundle-external-schema-names-and-user-conflict.yaml b/packages/core/src/__tests__/fixtures/refs/openapi-bundle-external-schema-names-and-user-conflict.yaml
new file mode 100644
index 0000000000..7a68a00946
--- /dev/null
+++ b/packages/core/src/__tests__/fixtures/refs/openapi-bundle-external-schema-names-and-user-conflict.yaml
@@ -0,0 +1,29 @@
+openapi: 3.0.0
+info:
+  title: Test ref with dots in component names
+  version: '1.0'
+  description: Demo
+  license:
+    name: DEMO
+    url: https://demo.com
+servers:
+  - url: http://demo.com/api
+paths:
+  /org-user:
+    get:
+      responses:
+        '200':
+          description: ok
+          content:
+            application/json:
+              schema:
+                $ref: external-ref-with-dots.yaml#/components/schemas/my.org.User
+    post:
+      responses:
+        '200':
+          description: ok
+          content:
+            application/json:
+              schema:
+                additionalProperties:
+                  $ref: external-ref-with-dots.yaml#/components/schemas/my.User
diff --git a/packages/core/src/__tests__/fixtures/refs/openapi-with-external-refs-pointer-conflicting-names.yaml b/packages/core/src/__tests__/fixtures/refs/openapi-with-external-refs-pointer-conflicting-names.yaml
new file mode 100644
index 0000000000..0f189eebc2
--- /dev/null
+++ b/packages/core/src/__tests__/fixtures/refs/openapi-with-external-refs-pointer-conflicting-names.yaml
@@ -0,0 +1,9 @@
+openapi: 3.1.0
+paths:
+  /foo:
+    put:
+      parameters:
+        - $ref: 'component-a.yaml#/components/parameters/User'
+    get:
+      parameters:
+        - $ref: 'component-b.yaml#/components/parameters/User'
diff --git a/packages/core/src/bundle/bundle-visitor.ts b/packages/core/src/bundle/bundle-visitor.ts
index cdb7b06446..480d87cec7 100644
--- a/packages/core/src/bundle/bundle-visitor.ts
+++ b/packages/core/src/bundle/bundle-visitor.ts
@@ -5,6 +5,7 @@ import {
   replaceRef,
   isExternalValue,
   isRef,
+  pointerBaseName,
   refBaseName,
   type Location,
 } from '../ref-utils.js';
@@ -12,7 +13,6 @@ import { type ResolvedRefMap, type Document } from '../resolve.js';
 import { reportUnresolvedRef } from '../rules/common/no-unresolved-refs.js';
 import { type OasRef } from '../typings/openapi.js';
 import { dequal } from '../utils/dequal.js';
-import { isTruthy } from '../utils/is-truthy.js';
 import { makeRefId } from '../utils/make-ref-id.js';
 import { type Oas3Visitor, type Oas2Visitor } from '../visitors.js';
 import { type UserContext, type ResolveResult } from '../walk.js';
@@ -274,27 +274,9 @@ export function makeBundleVisitor({
     componentType: string,
     ctx: UserContext
   ) {
-    const [fileRef, pointer] = [target.location.source.absoluteRef, target.location.pointer];
     const componentsGroup = components[componentType];
-
-    let name = '';
-
-    const refParts = pointer.slice(2).split('/').filter(isTruthy); // slice(2) removes "#/"
-    while (refParts.length > 0) {
-      name = refParts.pop() + (name ? `-${name}` : '');
-      if (
-        !componentsGroup ||
-        !componentsGroup[name] ||
-        isEqualOrEqualRef(componentsGroup[name], target, ctx)
-      ) {
-        return name;
-      }
-    }
-
-    name = refBaseName(fileRef) + (name ? `_${name}` : '');
-    if (!componentsGroup[name] || isEqualOrEqualRef(componentsGroup[name], target, ctx)) {
-      return name;
-    }
+    const [fileRef, pointer] = [target.location.source.absoluteRef, target.location.pointer];
+    let name = pointerBaseName(pointer) || refBaseName(fileRef);
 
     const prevName = name;
     let serialId = 2;
@@ -303,7 +285,7 @@ export function makeBundleVisitor({
       serialId++;
     }
 
-    if (!componentsGroup[name]) {
+    if (!componentsGroup[name] && prevName !== name) {
       ctx.report({
         message: `Two schemas are referenced with the same name but different content. Renamed ${prevName} to ${name}.`,
         location: ctx.location,