I can't progress some of the story because npcs I'm supposed to talk to I can't. From the forge the map says they want to talk but as soon as I leave that first area by using the door ways or the stairs the text bubble goes away.
I'm having this issue with Dax. I noticed something interesting about my situation though. The option to talk to her disappears as soon as I walk right in front of the fountain. I tested it to see where exactly I would lose the speech bubble icon on my map, and it's there in front of the fountain,
I had some of these issues. Here are some things that helped me. Sometimes missions are hidden underneath some of the map graphics in the expedition menu fiddling around with the map might reveal that you have a mission you need to do and maybe didn't know you had it.
Sometimes if an NPC wont talk to you, you can still pick up a mission from them on the mission board in the Launch Bay. Sometimes playing the game and doing other missions or progressing other stories will trigger whatever it is you have to do with another quest line. i got stuck on Matthius, so I did Brin for awhile, and eventually Matthius recognized me again. At one point I thought I had been done with all the quest lines and I was doint contracts, and legendary contracts, then suddenly Matthius gave me quest that continued/concluded whatever his story line was going on about at that time. So you may just need to go about playing the game. Get into other peoples squads and sometimes as you play the game in their squads it can unbug things going on in your game.
Sometimes you can unbug your stuff by starting another pilot and playing them for a little while.
Drin is notoriously hard to talk to, and sometime I've seen talk bubbles I can't activate that are just left-over, disappearing after I do another mission and come back.