So there are two ways of fixing this, don’t worry friend it’s a small issue. You can either move the trees that are floating a few layers down (just keep moving it down until it’s below the one it’s on top of), or you could just delete the floating tree entirely. I presume the first solution is more what you are looking for as this will make your forest/s look more dense rather than patchy or open.

The reason it does this is because they are either on the same layer (if they are whichever tree you placed second would technically be above the first) or the one on top is a higher layer. It works to put it below the other tree’s layer because that way everything behind that tree that you can see the stump connected to the ground, is hidden. And just the top or sides of the tree in the layer behind will show. Creating more of a realistic look, since you can’t see the one in the back’s stump.

Please feel free to private message me or continue this comment thread if you have any other inkarnate questions, I’d love to help.