Treecapitor is finicky. Sometimes the whole tree will come down, sometimes 1 block will be chopped out and then the second block will remove the rest of the tree. In extreme cases, i have had to chop down the entire tree and treecapitor doesn't ever show its face.
I happens and always has - treecap doesn't recognise some trees as trees and sometimes the tree detection is odd. Just try and get on with your life, machines do a great job of chopping down trees for you!