Also that point in the future era where you have to hold down three controller buttons in order to open a plot-critical door, but the emulator was only able to register two at a time. That one frustrated a lot of folks.
(I know this post is old) That wasn't the emulator being wrong, at least not for me because I finished the game. Instead it was how keyboards couldn't deal with more than [number] keys being held down at once in key-cluster, I don't know if it was a PS/2 issue or something. The solution was to temporarily remap a joypad button to another key.