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.
Plot hole: A few days after deploying, Ronnie returns home due to being discharged from the National Guard because of his anxiety disorder. In reality, being medically discharged could take months or longer, depending on how long it takes the Army to decide on follow-up medical care and possible post-discharge disability compensation. If the Army suspects that he concealed an anxiety diagnosis before he enlisted, that could result in an additional investigation for possible fraudulent enlistment charges.