I had the same thing happen to my lovely Pearl Izumi shorts. They were black with red stitching and matched my bike/outfit perfectly.....sigh.
I found the culprit: My saddle wedgie!
I had changed to a slightly larger one to accommodate my cell and pack-lite but the velcro strap had a corner that curled out. As the wedgie was slightly wider than my old one, it rubbed the back of my thigh at the extreme pedal down-stroke. I wasn't aware of it until it wore a hole.
I have reverted to my old wedgie and have darned my shorts - the padding is too good and they were too expensive to discard!