yes! this happens in my yard every time the irrigation runs. the lowest head in the zone drains the system. i can live with it.
also, a valve that is not fully closing could cause this as well, but i would expect it to never stop if that is the case.
if you wanted to rule out the controller complete, i would suspect that running the system for 2 minutes then pulling the plug on the unit, that will take the controller to completely rule out.