I generated a new world and spawned next to a jungle. I flew into the jungle and saw a cut tree. I destroyed it, because I thought, it's a glitch. Near it, I found another!
Every time, vines are placed at this block, where the stem of the tree has to grow.
Steps to reproduce:
1. Generate a new world in 13w38c
2. Search a jungle
3. Sometimes you see cut trees, combinated with vines.
At huge trees, the branches are cut like the stems of normal trees.