No, the thing with the audio is normal. I’m seeing the same. “naked” AAC files don’t have accurate time stamps in them.
As long as the audio stream is not excessively longer than the video, this should pose no problem.
Another thing which comes to mind is that the video stream is perhaps damaged near the end.
Play the file in VLC and see if you can live withour the last 1 – 3 seconds of it.
If yes, use again MKVtoolnixGUI to cut the file around a time stamp near the end.
See [HowTo]: splitting multi-episode files with MKVtoolnix GUI for a How-To.
