Story missions bugged out on 2 separate parts of chapter 3, the secret weapon and rebellion, and on the Viper's nest under chaos undivided. Each time it failed to recognize new clues I had found as well as not giving me my loot when I completed the mission. It let me complete the missions so I can't replay them to try and re-acquire the clues so it's not showing any more missions for me to proceed to. 

Psn tag: turbojebus33

Character name: Azrael