I am componentizing one of my apps. I copied the app into a component and deleted all of the non-relevant components from the workspace. There were still several components in the component list that were no longer on the app. I noticed this when I went to delete unneeded queries and they complained of dependent components which were not there.
That is very strange, are you still experiencing this issue? If so, if you can provide an export of the affected app, I am happy to take a look!