You mean Alien: Resurrection right?
Because Alien: Isolation is a game from 2014 and was released for other systems (like PC, PS3, PS4, Xbox360 and Xbox One).
I just tested it with Alien: Resurrection and i figured out, how to solve the problem, you described.
When in the game, go to the RetroArch Quick Menu by pressing Hotkey + B (= X-Button on PS3 Controller), then go to "Controls" and there you set "User 1 Device Type" to "RetroPad w/ Analog" and "User 1 Analog to Digital" to "None".
Now the controls in the game should work correctly.