Did a little online research on Army Corps of Engineers and their work on various dams and levies in the Mississippi valley a while back, mostly from 1930s and 40s. Typical for them to remove loose of compromised material (rock) and use it for levy building or to fill in 'bypass' or shortcuts the rivers had made in the past. It looked to me that they made sure the channel stays clear of material over the years and assures where the water would flow in a flood event and not flow through the bypass. Why it would matter on a creek behind a dam I can't be certain. I'm don't know much about hydrology.