Most of content you mentioned unlocking after training ground found. So you need to find Nyun in lab first. After saving her talk with AMI and just rest in lab to trigger Nyun come back. Alpha will come when Tali go damp the heat from turret after you unlock the path to second vent part.
Hello. I have this same bug, or whatever it is. I rescued Nyun, slept, talked to Ami, slept, talked to Nyun (the scene Tali tells her to put a shirt on), unlocked both the exit and the "red" vents and Nyun never appeared into the Lab. If I exit vents she's back on the bar, but talks to me like she never was on the vents. If I talk to other characters, they ask me when Nyun comes back.. I've slept at least ten times on the vents Lab and a couple dozen times on the Med Bay, and Nyun is just completely gone from the Lab now. I can't send her or Ami to find resources, and I can't get through the second white-blocked-door because of this. The training grounds won't open, and even the Zeltan propose+wedding thing is locked out. I met with Alpha, but that is the only "new scene" I've had on this playthrough since I rescued Nyun, so the game is really stuck.
This is my fifth start-over and I've never had this issue before, although I've played in my opinion the same way I always do. I don't know what triggered it, so I just have to roll back a few hours and hope it doesn't happen again so I don't have to start all over again.. :/
Edit. The game tells me to explore the vents to find a way to the bridge. If I had to guess I'd say it switched into that as soon as I opened the red vents, and that probably is the reason I can't find Nyun on the lab. The game kind of soft-locked me out of other content except the ending and the random encounters on the vents. It didn't use to do that before the end battle was implemented into the game, for obvious reasons.
