When the fuel level is low on a pump submerged and cooled by liquid,
the "net positive suction head"
at the suction inlet of the pump becomes low,
and there is a greater chance that
the liquid will begin to boil and turn into a gas at the point in the pump passages where pressure is lowest.

As this newly formed gas bubble moves through the pump it suddenly encounters a much higher pressure area,
and the gas bubble VERY rapidly collapses and turns back to liquid.
This is "cavitation" and it can rapidly eat away metal and ruin a pump,
but it also immediately stops the pumping flow until the liquid cools down.

On a 1995 Ram Magnum 5.9V8 with 183,000 miles on the original submerged fuel pump I had this happen on a 1100 mile trip to Florida.

When i changed the pump I found the situation was made worse because the "sock filter" below the pump suction inlet had become clogged. The fuel filter above the pump on the 43 psi +\- high pressure side appeared to be still flowing without too much pressure drop. The pressure regulator above the fuel filter probably heated up the excess fuel it recirculated back into the tank too.