Amethyst geodes can generate thorugh the End portal room in strongholds, potentially causing the End portal frames to be missing or replaced by other blocks.
How to reproduce:
Seed: -341133055506249258
Coordinates: /execute in minecraft:overworld run tp @s 10893.67 41.25 9545.98 -136.20 34.20
This appears to be a duplicate of MC-205250. Please see this link for further details regarding this problem.