Locked doors Zalyssija, Malachite and Tech Tunnel.

[pn]

During my first playthrough of the game, I didn't have any serious bugs that would prevent me from playing. Now, during my second playthrough, I have a problem with locked doors in three locations.

Zalyssija - I can't complete the side quest;
Malachite - even though I have the access card, I can't get in through the door, I can get around it through the tunnel;
Duga Tech Tunnel - there's no other way to solve it and I can't continue the story.

Does anyone have a solution on how to get into the tunnel?
I sent a bug report to GSC but no response yet.