Continuity mistake: When Gomer Pyle is in the toilet with his rifle and after shooting the drill instructor, Pyle sits down on the fourth toilet seat from the back of the room. In the next shot where Pyle kills himself, he is sitting on the third toilet seat. You can see this already from the front shot of Pyle when he kills himself because there is a rise in the wall next to the third seat, which is visible through the whole scene. It is more obvious in the following shot where you can see the row of toilet seats and Pyle sitting dead on the third one. (00:43:00 - 00:43:35)
Chosen answer: A Drill Instructor is always mad at the recruits in order to forge discipline. Private Pyle was the biggest screwup in the unit, thus creating more work for him.
Captain Defenestrator