I found out about this while doing one take of my video about trapping the Chaos Guardian from DE.

Apparently, if you remove the crystal from the altar while it's freezing everything including itself, sometimes the timefreeze field will not dissipate even after waiting and breaking the altar will yield another identical crystal to the one you just pulled out. In fewer words, duplicating it.

I am finding it very difficult to reproduce this bug.

In fact, doesn't seem like a mod bug, but a software issue. It seems Minecraft crashed on the right time causing the crystal to duplicate.

Closing this now.