Thanks for the file. I can see the issue is caused by using Edge Boundary Checking mode. In this mode, elements that extend beyond the spline are removed. Whether an element is removed or not is determined by the location of its lowest vertex. What can happen with trees is that all the leaves are removed, but the branch, whos lowest vertex is still inside the area, is retained. To fix it, change the Boundary Checking mode to Size or Point.
I hope that helps,