so i think i pretty much told you everything in the post bwlow but i will try to give you an example.
at some point in my run i got a quest to investigate amelia but i never had the option to do so, because i didnt get the call from agent. now this made me unable to complete this quest, or any other with amelia because i cant go further. this has happened to me similarily with dana in a previous run.
i would try to playtest your upcoming patches more, so you can spot a bug like this, because it happens a bit later into the game, so i understand if its harder to spot. thanks for reading through.