Overworking bread dough by hand
Probably not. The enzimes in the yeast and flour break down among others the gluten, which is responsible for the dough structure.
Some reading material on enzymes


  Too much protease activity would break up the gluten, destroying the network that forms during kneading. A little bit, however, softens the dough and makes it more workable. If the dough is allowed to autolyse (i.e., rest) or if preferments are used, proteases have time to work before kneading, making the dough easier to knead. 


I would say this is rather "over-leavening" than overworking. (Over-leavened breads stay usually flat.) But the additional punches probably also helped breaking the remaining gluten chains.