I've removed an extension from a "Setup" profile, now all sites that are using it show as needing to be updated, even after I published to all environments. They always show the same "removed extension XXX" in the "Your changes section". Is this a bug? or am I doing something wrong?
Once you remove an item from a library (lib- profile) and save/published the changes in the library, any linked profiles need to be published in order to inherit the change from the library.
In other words, even though you've made changes to and published the library the linked profiles must be save/published to inherit the change.
Until this happens you will see the changes being inherited to the profiles on subsequent opens.
If you have published all of the linked profiles subsequent to the library change and you're still seeing the prompt to save/publish then you should contact your account manager to discuss the issue in depth.