I have had the same issue. It appears to be a delayed check from when I completed "The Theorems of Pandgram" using stealth. At the time, I was surprised that no one went hostile, because it wasn't the smoothest stealth job, but I had no issues, so I proceeded with my game. Now, ten hours later, I cannot complete "The Parable of Wael" quest because of it. It's a little disappointing, but hopefully will be fixed in the upcoming patch.