During the sidequest "Open Your Eyes" after I get the colored bomb and return to the fision tower, the dialogue that completes the mission does not appear, making it impossible for me to complete it regardless of how many times I enter and exit the tower

I assume this happens when you started the quest but advanced the main story before finishing it. Since the events at the tower include things that have to happen before a certain point in the main story, it becomes unavailable after hitting that point. I'll check if I missed something, and make the necessary dialog and trigger available to take care of that issue.