When I go up to where an ender crystal should be, I only see a flame. I can't destroy the flame with water and I can't replace the water without commands. The water and flame will continuously replace each other, causing a bit of lag. When I place an ender crystal on bedrock (not where they should be, just on random bedrock) they break just fine. If I place them on the towers, the crystals are again replaced with fire. I can break the bedrock and the fire will go away, but as soon as it is replaced with any block it will become re-lit.

To replicate:
1- Quickly build an end portal and go in.
2- Fly up to the ender crystals. They should appear to be fire.
3- Attempt to break the fire without breaking the block below.
4- Break the block below, wait a few moments, and replace it. The fire should re-light.
5 (WARNING: CAUSES LAG)- Place water above the fire. The water will not extinguish the fire and will instead flicker between water and fire until either the block below the fire or the water block is destroyed. (I could not place blocks around the ender crystals unless it was in a location where blocks had previously been or I was placing a water block).