Well this was a tricky one. But managed to repro and fix! Basically as the player and heretics are running the same pathfinding etc, the heretics were also running the cross fetching checks and sometimes overriding the fact that player got it. So I think theoretically they could have also activated the cross.
And thanks to trying to find this, found and fixed another unrelated bug with the heretics on boss level. Thanks again! ❤️