Anticlimax Boss: Count Chuck spends the entire final battle asleep. Once you kill all the bats guarding him, he is completely unable to hurt you.
Big-Lipped Alligator Moment: The dragon in the fourth stage. More blatant a BLAM is the witch disguised as a princess in the castle of episode 2.
Breather Level: Part Two Level 4 is a very straightforward level with no hidden areas and simple jumping puzzles, and it comes right after two complex maze-like levels and a boss fight.
Nightmare Fuel: Johnny will need a lot of counseling once he is done with his adventure. 10 year old kids are not meant to fight zombies nor to see spikes with entrails still on them.
Suspiciously Similar Song: Several. The title screen sounds similar to "The Monster Mash", the first stage contains the intro to "Toccata and Fugue in D minor", the penultimate stage of episode 2 has a small snippet from "In the Hall of the Mountain King", and the fight music against Igor bears similarity to "Flight of the Bumblebee".
That One Level: The two swamp levels in episode 3 are probably the hardest ones in the game. Expect to use that extra lives cheat a lot.
Stage 3-3 in particular contains some of the hardest jumps in the game: onto moving platforms that are very difficult to stop incoming.
Fridge Logic: The Putting the Band Back Together premise makes less sense when you consider that Frankenstein has yet to assemble his monster, and some of Igor's lines imply that he's not simply relocating old parts. It makes even less sense when you realize the Monster is being built after the Bride of Frankenstein!
That One Sidequest: Activating Lyman's Lament the normal way requires 44 shots to the scoop in one game. This won't happen until you have near-perfect control of the ball and can effortlessly pass the ball between flippers. (Or, if possible, removing the glass above the playfield and manipulating the ball by hand.)
Entering a flipper combination with at least one credit on the machine negates the need, but tread cautiously when playing at an arcade. You won't get the bonus multiplier boost, and the per-switch bonus is much lower. Feel free to do it on The Pinball Arcade, thoughnote though you can only get the related Wizard Goal by activating it the proper way.