You're only missing 3 eyes in the Prophecy dungeon. https://www.d2checklist.com/3/4611686018484423223/checklist
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I distinctly remember getting the first 3 in prophecy... looks like the first eye must have bugged out. Hopefully it will be there on my next prophecy run. I also never shot the eye in the green room, so not sure what happened there... I appreciate the reply, thank you!