I was flying around the minecraft world when I noticed a Mushroom Tree have no stem. I provided some images that include cords and seed
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it also happens to normal trees

This is just part of the natural generation. It happens when a giant mushroom or a tree generates over a water lake and so the water overrides those blocks and that is why they are missing.
Thank you for your report!
We're actually already tracking this issue in MC-610, so I resolved and linked this ticket as a duplicate.
If you would like to add a vote and any extra information to the main ticket it would be appreciated.
If you haven't already, you might like to make use of the search feature in the future to see if the issue has already been reported.
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