With a "pond" that is 1 block deep, you can fly into it from an angle and you go inside of the bottom, so your head is in the water when really you should be standing on the bottom. This corrects itself after a few seconds though
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I'm not using an elytra though. I;m in creative mode and flying into it at an angle I can stay inside the bottom block by holding shift
That's how elytra works, unless you're talking about spectator mode.