Note that I'm not the official voice here, but I think maybe a video could help make things more understandable.
Because if I add a folder to a collection, using the "Sub collections" option, all the subfolders are not seen like filesystem folders anymore, but as sub-collections. So (at least on my side) they have a different context menu, and no "Remove from Collection" entry.
If I use the default Delete Menu > Delete button, I can remove it just fine, so it might be worth checking what command the button you're using actually has.
Edit: I think you're referring the "Remove from Collection" button from the default Delete menu.
That run Delete REMOVECOLLECTION and in this scenario doesn't do anything, and IMHO is correct, because as I say above:
using the "Sub collections" option, all the subfolders are not seen like filesystem folders anymore, but as sub-collections
So when adding items to a collection that way, you want to use the "Delete" button instead, or just edit the button to Delete REMOVECOLLECTION=auto.
Hope that helps!