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.
Works for me. But I still think it's a better episode than watching William Shatner piss away an hour mooning over Joan Collins.
And as far as the engineer for that episode goes. It was never stated that that lady was the chief engineer. She could have been a "chief" in the same way that O'Brien was. Remember that was his title on TNG, and he wasn't the chief engineer. The woman could have been in charge simply because Scotty was off-duty.