This bug is a long time in game now. When you are walking trough a 2 block high way, while having elytra equipped or earlier equipped and you jump you are in the block above with you head. When there is a 1 high block gap, then you can walk trough this gap, but you are in the block above, while walking through it, after some seconds, you get damage. When reconnecting to the world, its fixed.
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Yeah bro is bug is sometimes very annoying. This only happens on player. This happens with me a lot.
Hope fully it will be fixed!