If you have a pressure switch on the pump that should work if it's wired in properly ie in line with either the positive or negative. It might just need a little tweaking, there should be a screw on the switch that will adjust the pressure that the pump stops at.
If the flow controller has dead end detection then the pessure needs to be set properly on the flow controller. That would be done by either pressing a sequence of buttons or by a dial on the inside.
The other thing it might be, it air before the pump and in the pump, that would cause a pump to continue.
Simon.