I have already posted about a similar bug on the tchort institute quest line: if you fail the interview and are forced to fight your way through, the game doesn't acknowledge that this quest is failed.
The same happened during the protectorate quest line: after learning that the CAU wanted to use a mutagen on the free drones, my character turned on them and destroyed the entire fort apogee base. Again, the game doesn't acknowledge that, the quest to plant the mutagen in the free drones hideout remains open. Unfortunately, because of this, the game also assumes the character remained allied with the protectorate:
Not only doesn't it make sense, it's pretty disappointing to get such an ending.
