Continuity mistake: When Joker goes to see Cowboy and the squad are sitting in the temple, the dead Vietnamese's face can be seen without the hat covering it. When the photo is taken by Rafterman, his hat appears and is removed.
Continuity mistake: Just before the jelly doughnut scene, as Hartman is walking up the aisle, he is in front of Joker's locker, about to reach Pyle's locker. A moment later he comes to Joker's locker, before he gets to Pyle's.
Continuity mistake: When Hartman slaps Joker, Joker's head is turned sideways by the slap. A moment later, he is looking straight down.
Continuity mistake: During the scene where the Joker moves into the building to kill the sniper, the sniper sees him and starts shooting at the pillar he is behind. During this shot, large chunks of the pillar fall away, but in the next shot, when the sniper gets shot, the pillar is intact.