1. create a directory named "whatever" 2. in this directory create an empty file named "whatever" 3. click the file, ctrl+x 4. go up one level to the directory containing the directory "whatever" and try to ctrl+v the file manager doesn't distinguish between a file and a directory of the same name, so it wants to overwrite the directory with the file (absurd, isn't it?)
This has nothing to do with the file manager. A directory is just a special kind of file, which contains a list of name/inode mappings. So, in the Unix world, directories are indeed files and as such, your mapping of names to inodes cannot have two entries for the same name, for obvious reasons.
BTW: The Thunar manual contains a brief introduction to Unix file systems, which you might want to read to get started.