Just encountered a bug during the "The Archwing" quest, when I got to the part where you have to start two generators. The first (right from the room entrance) one went fine; I hacked the terminal and the quest progressed to the second generator. However, when I hacked the second (left from the room entrance) terminal, it didn't do anything. It simply kept giving me the option to hack it again, but didn't progress the quest.
I've waited and waited, and after a while enemies stopped coming and it still didn't do anything. I haven't tried restarting yet, but it seems that that's my only option right now.
Update: It only happened the one time, once I restarted the mission, everything went as it should. I'm unsure of exactly what happened that caused it, but it could've been that I picked up the Archive before entering the portal. That's the only thing I did different the second run through.
