So, not sure how this happened:
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I planted an Amaranth sapling so I could get some purple fence posts (because purple), then went on a bit of a walkabout to add more pages to my Atlas. Came back and the tree had grown - like that.
I've had trees that grow without the base block. Likely some weird kind of ghost blocks where you're missing tree trunk. Put some dirt or something in the gaps and break it and you should be fine.