These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Shocking Swerve: There isn't much buildup for The Reveal that Salzella was murdering people as a second Ghost, and Salzella's motivations do not make any sense whatsoever (he has been stealing lots of money, but that's more due to clever accounting than his antics as the Ghost). However, this is amidst characters saying that nothing in opera makes sense and it comes across as extraordinarily meta, especially with the scene mentioned under Lampshade Hanging.
It would seem that he was originally trying to frame Walter for his actions to cover the tracks, and use the murders to do so, but getting badly carried away in the process.
And the villain pretty much explains at the end that the murders were because the victims had found out his identity; the rat catcher was blackmailing him and the music director had seen him.
And when asked why he didn't just leave the opera, as that would solve all his problems, he simply acts like that would be inconceivable, and doesn't get a chance to elaborate further.
There is build-up to the fact that Salzella is up to something that has to do with the accidents in the Opera House fairly early on (via internal monologue — he compares milk going sour to the situation in the Opera House with the comment that Opera Houses unlike milk doesn't go sour on their own, and phrases it in such a way as to make it clear that he's the one making things go sour). Still not much, since it is a single easily missed line (there is more foreshadowing to there being two Ghosts, however).