Creating a file “foo” when there is a directory “foo” asks the user whether he wants to overwrite the “file” (which is actually a directory). It seems more appropriate to just show an error because overwriting directories can cause significant data loss.
Renaming/moving a file while the properties dialog is open closes the properties dialog. It would be nice if the dialog updated itself instead of being closed.
With the path bar enabled, renaming the current folder sometimes makes Thunar act weird: the last path bar button is removed, the directory content may become empty and if you have the parent directory open in a window at the same time, the directory entry is removed from the view.