Have you been doing search and replace? This function can cause things to go sideways fast. It may be possible depending on your source that undisplayed characters might cause a problem.
Is the problem isolated to just this one file? Is there another you could try to see if this particular file is troubled? If it is a cheesed copy of a copyrighted book who knows what is in it.
You can probably get back something of a copy by running the .mobi through calibre. At least that way there should not be anything wrong with file except too much calibre stuff in it...it is ugly, but functional.