Audio problem: When Brian escapes his room and the headmaster with security is checking the rooms, if you look very carefully while the camera is going to Brian's room, you can see the headmaster hitting the door with his hand out, but the sound sounds like it would if he were hitting it with his fist.
Other mistake: Just before the bus comes to pick up Brian, he reads the brochure and says "The Perfect School; why settle for anything less than perfect?" but on the brochure, it says "With perfection, all things are possible."
Answer: Whoever created the Masked Mutant comics would still be around to create other comics even with the Masked Mutant dead and the Galloping Gazelle retiring, so Skipper could still receive different comics with all new characters. When Skipper goes into the Masked Mutant's lair, he is hit with a beam of light that turns him into a comic book character so after saying that he's the Colossal Elastic Boy, he turns into the hero at the end of the episode.