Anarchy's End I not triggered & Metamorph organ missing on Basilica map run

I finished running a Basilica map where the Anarchy's End I prophecy triggered. However, upon clearing the map, I didn't didn't finish (The prophecy states that you will find a rogue exile in a map that will drop a card). I killed a rogue exile, but a card didn't drop and nothing signaled a completion of the prophecy. In addition, an eye organ didn't drop for the area (There were 5/6 eye organs). It looks like a rare was missing. There was a breach in the area as well, if that matters.