Gotta remember to start saving before hitting unmarked switches.
During the mothership zeta quests I hit a button next to a door that i assumed was for that door. Nope. Set off an alarm and was immediately swarmed by aliens and drones. Didn't die but wasted a ton of ammo and healing items with not much to show for it.
I will say these alien weapons are much more powerful than what i was using. Should make the game quite a bit easier from here on.