Another fault I discovered was that one of my followers' horses was actually invisible and I ran into it several times and I could hear it. (The exact oppisite of the first bug).
Fast-travelling seemed to fix the problem and when I turned the 'Spectral Fade' back on (for when followers get off their horse) the problem has seemed to stopped.
I have a feeling that it is a script-error or something along those lines. Please let me know if anyone else has had this problem or similar, and then we can inform the author.