Fanon Discontinuity: The sequel, where the first game's director wasn't present. According to Word of God, the publisher (Interplay) got an opportunity they had pestered him about to make a game they wanted, and the result was a buggy, tonally-inconsistent and generally almost unplayable mess of a game that no one even gives an inch of positive opinion. And it crossed the line by abruptly killing off Lester.
HSQ: Extremely high, the whole game is basically one cool thing stacked onto another cool thing from start to finish.
Narm: The punching sound effect sounds more like slapping. The animations where an alien beats Lester into submission, or when Buddy gets into a fistfight with another alien don't help, either, making it look like everyone is just getting into intense slapfights. This is possibly a case of Reality Is Unrealistic, as the punching sound in your average action film has some extra sounds layered over it to make it sound meatier.
Nightmare Fuel: The sudden apperance of the Beast very early in the game, and the enusing chase. Though you're more likely to get killed by the slug-like creatures that you have to run past.
The tentacles that grab you from above (think Barnacles from Half-Life) and the "pits of chewing teeth" on the floor in the Cave section of the game. Getting caught by one of them will show an animation of their teeth closing in on the screen.
Porting Disaster: Comparing the Sega Genesis and Super Nintendo versions of the games, both feature a new sound track and are harder than the ports before it. While the SNES version has better audio quality, it lacks in performance (the game will slow down a lot of times), and load times, despite being a cartridge-based system! The Sega CD version does rectify all the problems from both (even the load times, despite being on a system notorious for these).
Some may consider the 3DO Interactive Multiplayer version to be this. Despite some nice visuals and a good sound track, and teasing the fans with a sequel, the common complaints included the updated backgrounds and soundtrack not fitting with the atmosphere and what is going on in the game. Also, the sequel was never released on the 3DO.
Sequelitis: The first game was great, but hard and yet forgivable. Heart of the Alien is a lot harder for the wrong reasons, and looks comparatively worse than the first game. Having stiffer controls, and challenges based around these controls, really didn't help this game. The big thing that saves it is its inclusion of the best console version of Another World at the time, complete with the best soundtrack for it.
They Changed It, Now It Sucks!: Some people complain that by making the background more detailed in Anniversary Collector's edition it ruins the minimalistic art style that makes the game so atmospheric. But that is nothing compared to the 3DO version which has a very generic sci-fi feel to it. Though the 20th anniversary edition averts this by providing the option to play the game in the original graphic settings.