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.
(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.
(at around 1h 19 mins) After Dracula chases the plane with Johnny on it, he crashes into Mavis' room and returns to his human form. When he appears through the smoke, his face is sunburned and there are hole burnt in his cape. In the very next shot, his skin is its usual pale white color and his cape is intact. What actually happens is that his cape,clothes and skin can be seen repairing themselves.
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.