(at around 45 mins) When Mavis and Jonathan are on the roof, watching the sun rise, the lower portion of the roof becomes lit by the sun first, leaving the upper portion in shadow. A real sunrise would light the roof from the top down.
In the first chaos scene after Johnny enters the hotel (when he realizes the monsters are real) a fly is depicted with multiple eyes (like a fly would have). in all later depictions of the flies, they have human-like eyes, with whites and pupils, etc.