When shuffling free standing items into the item pool I have noticed some spawning issues in certain areas. They will be vanilla until you re enter the area (sometimes it will take multiple re entries before they spawn the shuffled items). Areas I've seen this happen in are the green rupees at the bottom of Zora's fountain and the Octorok grotto in Gerudo Valley.
When shuffling free standing items into the item pool I have noticed some spawning issues in certain areas. They will be vanilla until you re enter the area (sometimes it will take multiple re entries before they spawn the shuffled items). Areas I've seen this happen in are the green rupees at the bottom of Zora's fountain and the Octorok grotto in Gerudo Valley.