That is due to a glitch introduced into the program last year, which TTax has not fixed.
The filename preceded with a tilde (~) is a duplicate file that is was created periodically while you were preparing your return and was intended to be used if the program ended 'unexpectedly'. If there were no unexpected program terminations the filename preceded by a tilde was supposed to be deleted --in prior years this was all done silently in the background.
If you carefully inspect each file, the file WITHOUT the tilde should have a later modification date and time than the file with the tilde; it may even be a larger filesize.
If you have any doubt you could open each file using the version of TTax that created the file(s) and compare them manually for correctness.
I have not heard of any cases where the tilde (~) prefixed file was the correct file to be used --UNLESS the non-tilde file canot be opened for some reason.