Marmalade's mouth never moves in the film even when she is heard "talking" onscreen. This is intentional.
Spunkneck's lines do not match his lip movements when he is seen driving his car. This is intentional.
There are several points in the film where you can clearly see the puppeteers hands moving the dolls around.
Marmalade is very obviously wearing a swimsuit during the bathtub scene.
Several of the "nighttime" scenes in the film are very obviously shot during the day, as indicated by the blue filter on the scene, revealing the use of a blue camera lens to simulate night.
The coffee cups that the Doll Fixer is drinking from are very obviously empty.
Gilbert visibly blinks in the ending scene, even though he has been turned into a human doll.