Toward the end when Alex is being punched by the "Puppet Master" his mouth is bloody. Then Megan smashes a vase on The Puppet Master's head, and in the next shot Alex's face is no longer bloody. In the next close-up of him the blood has returned.
When Dana and the puppy is walking on the corridors, she's holding the dog on the right hand and the bottle is on the left hand, when they swap to a new scene the dog is now suddenly on the left hand and the bottle is on her right hand.
(at around 5 mins) When the puppet Blade is racing around the Bodega Bay Inn grounds, he runs towards the street and stops at the curb just when a car nearly runs him over, and we see the side of the tire. But when the door opens and the two assassins walk out, we see nothing near the car where that doll should be, nothing even close to the car. After that overhead shot, the POV shows him running from behind the tree but there was no time to get there.
In the beginning, when the puppet Blade is racing around the Bodega Bay Inn grounds, he runs over to a pulled up car. When the door opens and the two Nazi assassins walk out, you can see three crew members in the car door window reflection; two of them are down on their knees operating the camera in place of Blade's bird's eye vision, while the third is standing on the grass watching over.
When Dana is walking down one hall with Leroy and a bottle of champagne, the exit sign is backwards. Another indication that this shot was flipped is that the bottle of champagne and the dog switch hands in the very next shot; which isn't flipped, and was filmed in the same hallway.
When Frank is tied to the bed and being attacked by the puppet Leech Women, at first she does not have nail polish on but when she starts vomiting leeches she does. This is because two different versions of Leech Women where used for this scene. the string puppet and the puppet used to vomit the leeches, both the puppets where painted differently.