Strange visual dischordance
The live eye-performances being married to the puppets makes the animation of the inanimate object take on more of a lifelike presence - it tricks the mind into believing the puppet is something truly alive. So why did they counter that effect by giving the puppets sort of hideously inhuman features? It makes them into something alien and uncomfortable to watch. All the work of marrying the human elements to the creepy puppets ends up sliding straight down into the uncanny valley.
I love the effect, and like the film, but I don't understand that decision.