Multiple files with the same name cannot be trashed/deleted. ie. If a file named x.pdf is trashed. Another file named with the same name of x.pdf will not be trashed when dragged into the Trash icon. There is no error message or anything, there is just no response. The same occurs when you try to delete the second file with the right-click > "move to trash" method.
This seems to work for me. Check the latest version of nautilus from RAWHIDE
nautilus-2.8.1-2 seems OK in this regard. I deleted one file named test.txt, then another named test.txt. It renamed the second file to test(copy).txt. Setting to MODIFIED for nautilus maintainer to confirm.