I have two folders named "Music." One of them is for musicians' websites, and the other is in a folder called "YouTube" and is for YouTube channels with music on them. Sometimes when I move a feed into the YouTube music folder, it accidentally gets moved into the other music folder.
Unfortunately this is a known issue. You'll need to have unique folder names, even when nested. Just change it by a single character to fix it. It was a mistake I made a long time ago to not allow for unique names and now it's too late to fix it.
I've been messing around and I found a workaround. If you rename one folder to something else before moving feeds into it, you can change the name back afterward and it won't matter if there are duplicate folder names as long as you don't move feeds into it without changing the name again.