When Hesse is shot in the stomach by the Mr. Static toy - you can very clearly see the squibs under his shirt, which then explode for the bloody effect.
During the scene where Baby Oopsy Daisy is drawing the circle around the security guard, you can see the puppeteer's hand for several seconds behind the doll.
As Grizzly Teddy is attacking Charnetski - mauling and biting him - you can see the puppeteers sleeve and arm in some of the shots (bottom right).