After clicking the starting crystal (the one that is visible before the Ossirian is pulled, it immediately respawned, which is apparently not something that is supposed to happen.
The respawned crystal was unusable (won’t debuff Ossirian when clicked) and it appears that whatever crystal gets triggered to spawn from that unusable crystal is also unusable.
This was happening every attempt, so obviously, best to leave that respawned starting crystal alone. It did seem to reduce the number of available crystals though.
Others in raid said that other crystals as well weren’t working properly to debuff (but I can’t confirm that since I was off to the side clicking ones that were super far away trying to get them to respawn nearer to boss).
That’s been a bug literally forever. It was just as annoying in 2006 and you learned to work around it.
Did AQ20 on Friday and we ran into a crystal bug too.
We clicked the crystal near the stairs, then went back and forth between the crystal on his left side and another crystal near it and back to the crystal on his left side.
Then we encountered a “double crystal” where two Ossirian crystals were taking up the same 3D space and Z-Fighting was happening if you mouse over the crystals. Even while clicking on it, it just got activated, then went down again without taking off his supreme mode buff. That may be the same bug you’re talking about.
This just happened to our raid. Confirmed March '21.
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Also this is BS. You can’t work around it. Every crystal was bugged for 5 attempts.
Same thing happened to my raid last lockout, too.
Also, grats on getting your pally to 60! 
THis happened to us today as well as a few months ago. Hoping for a fix. Thanks.