Catherine I am trying to recall what my teacher used to say about these problems, so it might not be a very accurate recreation of her explanation. According to her all the anxiety and stress are concentrated in the diaphragm making it one of the first body parts to be damaged. So the fragmented breathing and body movement is most likely tension gathered there from stress.
The good news is that when I progress into the exercise these fragmented movements fade away gradually. Also the meditation has the same effects relaxing my nervous system.