Broken Base: There's no real consensus on whether the Capcom adaptation or the Virgin Games adaptation is the superior game, though either camp tends to acknowledge that the other is still a good game in its own right.
The music in Jaffar's Palace, which is very short compared to other songs, and loops pretty badly. Even worse, in the DOS version it keeps playing over the ending after you defeat Jaffar.
Nightmare Fuel: The infamous Game Over screen which was no doubt a source of nightmares among those who grew up with the game along with the movie. Running out of lives and continues treats you to Jafar brandishing a Slasher Smile against a fiery background, emitting an Evil Laugh with the words "GIVE UP, STREET RAT!" beneath him. Since the game never tells you how many continues you have, you can't see it coming unless you buy a lot of them or use the Classic Cheat Code to avoid seeing the screen. However, the next screen, which has the words "The End" and the Genie popping into say, "Made you look!", softens this a bit.
"The Escape", the level in which the cave collapses and Aladdin attempts to escape on foot, will floor new players and put veterans under pressure. It's the first level to introduce One-Hit KO hazards beyond pits (giant boulders), there are pits of lava all over the ground that are much easier to fall into than those of the previous stage ("The Cave of Wonders"), the roofs of the caves are so low that jumping over the lava pits becomes a matter of perfect timing, the color of some of the platforms is so similar to the background that you can flub some jumps by not realizing you could jump later... and the last boulder, even if you do manage to outrun it, can sometimes end up falling on top of you while you're on the carpet for the level-clear animation! To top it off, the game won't skip this stage for you like it will the immediately following stage, "Rug Ride", if you mess up enough times. The rest of the game is a breeze once you clear this level...
"Rug Ride" itself qualifies in the DOS version. In both versions, you're riding the carpet through a narrow tunnel, while trying to dodge One-Hit Kill boulders. The level slowly becomes faster and faster and faster andfaster until you need lightning-fast reflexes. There are no checkpoints, so dying will send you back to the beginning. However, while the Genesis version you'll automatically skip it after failing enough times, the DOS version has no such Mercy Mode. Good luck.
"Inside the Lamp", a.k.a the Genie level, isn't tough at all at first - there are no enemies, and no way to take damage - but the whole level is a bunch of Floating Platforms above a massive Bottomless Pit. Towards the end of the level, finding solid footing becomes increasingly difficult, and you have to perform a fair amount of pixel-perfect jumps. The most maddening moment is just before the end of the level: there is a very tiny genie hand platform, some pixels wide, that you have to jump on. Missing it means instant death and redoing several difficult jumps. The hand is also so low that it floats off-camera, and can't be seen unless you crouch.