Version Number Conflicts When Updating Main File Before Additional Files

If you update the main file e.g. to version 1.3 you can't update the additional files to the same version number. You get an error, the version number you put in is already the one the file got. So basically updating the main file, changes the version number for every other file uploaded (even if those weren't updated). So it would be nice, if version number only apply to the actual file they are made for. If you update the additional file to 1.3 and the main file afterwards to 1.3 it works, just not the other way around.