For example, if there were two Lazarus', where was the anti-matter Enterprise and her crew? In orbit around the anti-matter planet? That we didn't get to see THAT is the thing to be annoyed by, if anything is.
My theory is that we do
see the anti-matter Enterprise
in this episode; in fact, we spend the entire story on it. That's the only explanation I can think of for Engineering being completely different and for the Chief Engineer suddenly being someone who is very much not Scotty, as well as all the other little moments that feel a bit 'off'.
Doesn't make the episode any better, but it is a theory.