Plot hole: The opera house is directly above the Phantom's hideout in the sewers, with an orchestra booming loudly overhead almost every night (the Phantom plainly hears the orchestra), but this constant vibration doesn't affect the integrity of the subterranean structure. But at the end, the noise of two simple gunshots causes the Phantom's hideout and a massive part of the sewer system to collapse.
Plot hole: The show is about a NYC high school for the performing arts. Yet many scenes including the piano composition rehearsals, feature way older adult students in their 20s, even 30s.