I'm at the very end where you confront Ulysses, the quest says to deal with him, after a long dialogue we fight, I kill him. The quest doesn't update. " Deal with Ulysses " is still unchecked. I even tried disabling both the eyebot stations, nothing changed.

Is this a known bug? If so is there a way to fix it??

I thonk you have to do the rest of the quest to fix it.

that happened to me my first time through. i pretty much just had to wait a little while and the quest eventually updated itsself

Have you killed all the marked men?