* BreatherBoss:
** The second boss (Abominable Snow-Burns) is way easier than the first boss, Fu Manchu Burns.
** Ramses Burns is ridiculously easy. To beat him, you have to unravel his flying carpet by jumping and pulling a string (just causing Bart's sprite to touch the string "pulls" it). Only the very first jump is remotely difficult, as the string gets longer and easier to reach each time. In fact, once you've pulled it once, you don't have to do anything but stand there and jump, and Ramses' simple back and forth pattern will cause him to bring the string right to you.
* PortingDisaster: The version released for the Master System and Game Gear strips out all the storyline sequences, has even ''worse'' controls than the NES version, and strips the soundtrack down to just two short, repetitive tunes.
* TheProblemWithLicensedGames: It's definitely an improvement over ''[[VideoGame/TheSimpsonsBartVsTheSpaceMutants Bart vs. the Space Mutants]]'', and aside from the [[VideoGame/TheSimpsons arcade game]] and possibly ''Bart's Nightmare'', arguably even the best ''Simpsons'' game to be released during the 90s. But it still has a lot of control issues hanging over from its predecessor, and can be repetitive and NintendoHard at points.
* ScrappyMechanic:
** The controls in general. They're not quite as bad as often reported in that they ''do'' work right consistently, they're just unnecessarily peculiar. Like its predecessor, the game has the same control scheme where the same button is used for running and jumping, and so to take a running jump you have to hold the attack button and hit the jump button (which in this game, causes you to waste ammo every time you take a running jump). And Bart skids after taking a long jump, making precise jumps difficult[[note]]the trick is to turn Bart around so he's facing backwards as he lands - again, it works consistently but it takes a while to get the hang of, especially with the controls being so odd[[/note]]
** The "Find the bat in the coffins" minigame, for being based on [[LuckBasedMission pure luck]].
* SequelDifficultyDrop: While it's still NintendoHard by any standards, the difficulty's a lot more reasonable than it was in ''Bart Vs. the Space Mutants''. This time around Bart gets five hitpoints instead of just two, power-ups are much more plentiful, and the levels (aside from a couple of the latter ones) aren't nearly as absurdly long as they were in that game
* ThatOneLevel:
** Level 2-1 (Ice Cave): It's a giant cave of collectables that's very hard to find the right way out of. To get on the right track, you have to repeatedly ram into an icicle to create a gateway, which is never hinted at.
** Level 3-1 (The Pyramid). First there's the section with the expanding platforms, which are extremely squirrely. The moving platform, followed by the incredibly tiny platforms, just make it all worse.
** Level 3-2 (Valley of the Kings): The second half of the first section is a long vertical shaft with a dozen rooms branching off from the sides. The shaft is just too wide to be crossed with a jump. There is a single, non-replenishable Bartman powerup at the bottom, in a spot where you can only reach it by falling on it from above. Maggie and the Krusty Sand Skulpture are in one of the rooms. Have fun searching.
** Level 4-2 (Horror Movie Set). The coffin maze is pretty bad, but the endless, endless, ''endless'' jumping section at the end is pure PlatformHell.