You have a Fertiliser on the 3x3 farm? I get that a lot on my small farms too but found the problem to be easily fixed by having a slightly larger farm. For me, I had mine at 9x9.
What happened is that the Harvester harvested too fast and took out the base block together with another tree's last block. However, Harvester detects trees by detecting the base block but only start harvesting from the top. So now, what you got there is a tree that the harvester can't detect.
Having a small farm gets in the way since no other trees will grow because of the canopy, but having a larger farm means somewhere else, there's space for another tree to grow. And once a new tree grows, the harvester will detect that and starts harvesting EVERYTHING (that can be harvested) in an area larger than it's detection range, therefore getting rid of the floating tree.
What happened is that the Harvester harvested too fast and took out the base block together with another tree's last block. However, Harvester detects trees by detecting the base block but only start harvesting from the top. So now, what you got there is a tree that the harvester can't detect.
Having a small farm gets in the way since no other trees will grow because of the canopy, but having a larger farm means somewhere else, there's space for another tree to grow. And once a new tree grows, the harvester will detect that and starts harvesting EVERYTHING (that can be harvested) in an area larger than it's detection range, therefore getting rid of the floating tree.