I believe I'm also experiencing this issue, where Tixati is retaining file crusts for files that are not selected for download. I think this is also related to how tixati shows stored bytes/file progress for removed files. To give an example, I have 204 file crusts stored for one torrent, and less than 100 files actually selected for download. Here's an example of what I'm seeing:
Edit: I think I've found a workaround. If you have a torrent with "ghost data", i.e removed files that still show left over progress/bytes, then search for crust files that have your torrent base-16 hash in the name. Delete those files, then recheck the torrent. Any files that were set to "off" should now also show 0 bytes downloaded.