I'm sorry that this has caused some frustration for you! If this is the circumstance I think it is, then it's not supposed to be able to happen; there could be a programming fault in there that I need to address to prevent the scene in question from coming up after such an important Event scene. If that's what's happened, I'm doubly sorry; it'll be fixed in an update for sure!
I mean yeah if it's not supposed to happen after all the conversations you have with that specific character in the cargo bay then it would definitely lift the malaise that hit me after. Cause all the words exchanged and the honest feelings made it feel like they are super connecting to you and you are meaning more than just the initial scene. If it's true that it's supposed to disable that other scene if you made it that far with them, then I certainly would be a lot happier to continue.