1. I always presumed that the culprit in The Final Scene was crazy. As in, they had legitimate psychological issues surrounding the theater, so they literally couldn't think correctly. I based these ideas off of the endgame sequence, where the culprit talks about the theater, as if it won't be destroyed in minutes. That is major denial there.
Now, the game tries to explain how the culprit teleported across the theater during the kidnapping; one of the audio messages you hear was on an automatic timer. You can find this hidden in the culprit's area, at the end of the game.
I am not going to think about the creepy, creepy possibility that the culprit kidnapped Maya for reasons other than stopping the theater's demolition...
2. With Ghost of Thornton Hall, people question how Charlotte's ghost wrote Nancy's name on the blank tombstone in the graveyard, considering that she's a ghost. Her Interactive has confirmed that it was Harper who did that; Harper just doesn't take credit for it.
3. In general, Nancy Drew and the Hardy Boys go through a lot of life-threatening accidents. Usually, at the end of the book/game, the culprit takes responsibility for these accidents, saying they wanted to scare the detectives off the case.
Very rarely does anyone point out that attempted murder is a crime in and of itself. In most cases, murder is a much more serious crime than the crime that the culprit is trying to protect!
But then again, I'm willing to overlook some illogical felonies every now and then, because it makes the stories more exciting.