I get the same problem on perfectly normal sites,
reading perfectly normal HTML. Since HTTrack thinks it
downloaded them right I can't even update them to full
size. Perhaps some kind of 'after mirror verify' would
be a good upgrade to HTTrack? In my case it might have
something to do with the fact that I have a modem
connection and the modem drivers don't seem to be fully
stable.(ie. they might be dropping connections, and
losing the tails, perhaps HTTrack doesn't verify that
the transfer was actually completed, just that the
connection was successfully opened) 
In any case I have hundreds of shortened HTML files on
my harddrive. I suppose I could just delete them when I
run into them and rely on normal updates to fix the
problem. Or perhaps I could write a script to find and
delete incomplete files?