The short answer is that tup wants to know about all build artifacts, and thus, every output file must be specified. I don't know much about clang's side effects, but I guess on Windows it leaves this tmp file around. You'll need to account for that with your build command.
The easiest way is probably a flag to tell clang to not write it. If that doesn't exist, you can try removing it after the command runs (rm -f *.o.tmp in shell, but I don't know a good cross platform command that operates silently if the file is missing).
If neither of those works, then more information about what you want to do would be useful.
Hope that helps!
Erik