If you have disabled view of hidden files in your File manager, you wont even see them, but when creating, changing, deleting etc. Syncthing paths more than once, reinstall, backup e.g., there is a big chance you have a bulk of .stfolder(1), .stfolder(2), e.g. doubles bloating around.
A simple feature to remove old .stfolder entries before creating one would solve this right? This could be a permanent option for every new entry, because it may interfere when syncing to multiple devices or something.
Although the folder marker itself is created by Syncthing, these additional copies do not belong to it. I don’t think it will be wise to build functionality into Syncthing for deleting files / folders it did not create / does not own. You should take up that issue with whatever program is creating the copies.