A flow sensor is incorporated into a junk basket to sense a flow stoppage due to a plugged screen or plugged cuttings ports in a mill. The sensor triggers a signal to the surface to warn personnel that a problem exists before the equipment is damaged. The sensor signal to the surface can take a variety of forms including mud pulses, a detectable pressure buildup at the surface, electromagnetic energy, electrical signal on hard wire or radio signals in a wifi system to name a few options. Surface personnel can interrupt the signal to take corrective action that generally involves pulling out of the hole or reverse circulating to try to clear the screen or mill cuttings inlets. Other variables can be measured such as the volume or weight or rate of change of either and a signal can be sent to the surface corresponding to one of those variables to allow them to be detected at the surface in near real time.