Continuity mistake: There's an electrical outlet on the wall below the window (aligned with the window shade's loop) in Sid's room near the Megadork poster, but when Sid throws Woody to the floor and raises the shade (before he scorches Woody's forehead with the magnifying glass), that outlet has vanished.
Continuity mistake: When Johnny Cage is fighting Scorpion, and he does his human spear, Johnny runs until he stops at the tree. The spear then catches up, and becomes wrapped around the tree in front of Johnny. When the camera changes view, the spear is just leaning on the tree. The camera changes view again and the spear is wrapped around the tree again. When Scorpion pulls the spear back, it goes straight back, and doesn't unwind around the tree.
Continuity mistake: At the beginning, Nix threatens young Dorthea with a real madrill, but that's all we see of it. It's never shown being put away, and it's not there when Swann and his crew break in to incapacitate Nix.
Continuity mistake: In the scene when Junior cuts the tree with his chainsaw, when he looks up to see how high it is, we can see it has branches. In the next scene when the tree falls on Scoutmaster Flimm, it doesn't have them at all and is cut straight at the top. (00:29:40 - 00:31:00)
Visible crew/equipment: When Jeremy impales himself on the silver ritual knife, watch as the "knife" bends under the weight of his body - an obvious rubber prop.