In a number of VM plants there are "stubs" from where it seems that a branch or twig has been removed. This motif is apparently fairly common in other manuscripts. My guess is that since forests and trees in general used to be managed very intensively, people were used to seeing trees with cut branches. Might this mean that the motif might be a "tree marker" or "woody marker" in the VM?
Here's just two examples, from the Liber Floridus and MS Palatino 586, but it is certainly not limited to these: