This is a bug that happened on a video recorded by the brazilian YouTuber Hey Vordex (which is funny because this happened right after he was saying that bugs will be less common), so I test it on a different world, and sometimes, a tree generates without its log, and after that, because the log wasn't there, the leaves started to disappear. Here's the link of the exact moment this happened on Vordex's video:
https://youtu.be/2LZTKu8QGaM?t=213
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Duplicate of MC-125007.