Maybe N got bored and started using them inappropriately. Maybe his Pokemon were fooling around with his toys. Maybe somebody came in his room while he was away. (Also, you're trying to tell me that nobody told him how to use any of this stuff? Not even the goddess? They taught him about numerous amount of things, but not how trains work.)
Maybe the Rare Candy was in there cause he or his Pokemon, I don't know, likes to eat candy *shrugs*. (Seriously, you're really stretching.)
Maybe. I thought those two ladies were his friends but again, I don't know.
I don't claim to know what pain a person is in when a dragon that controls time, space, or dimensions destroys the universe but you don't either. You can claim that's painless but it's really a baseless claim, and I don't think even Cyrus knows.