So I believe it is the trolling motor. I witnessed this with fish on a very clear lake last spring. I was sight fishing giant schools of crappie and bluegills out deep along a weed line, and if I just let the boat drift over them I could fish right on top of them without any issues. If I even touched that trolling motor once, every fish within a good 10-15 yards of me instantly jumped and swam in every direction away from the boat for a little ways.