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.
When Dracula takes Johnny up to the hotel room with Glen's trapdoor, there's no shrunken head on the door. When he escorts Mavis out, there's now a shrunken head there. This head also has the same voice as the head on Mavis' door.
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.
As Dracula heads up to Mavis' room at the beginning of the movie, he passes by a number of other hotel rooms. The last door he passes, the witch/maid greets him, and the head says, "Maid, clean up this room!" You can see the number plate on this door, room #174. Later, after Mavis' "trip", Dracula approaches her door, and we can see the number plate, room #174.
While Eunice is playing Bingo, and has five cards infront of her with different dot patterns, all the cards have exactly the same numbers in all the same positions. When the shot pans to the old monster next to her, she also has the exact same bingo card.