When the monitor shows that red light for battery voltage (all it is, is a coarse voltmeter--each colour is for a band of voltages between 12.7 for Full on down) then check the battery voltage at the battery with your meter.
What is the "high set point" voltage in that ASC? 13.8 is low voltage for an afternoon reading on a sunny day--should be 14.x. --unless voltage was still climbing through 13.8.
Some ASCs have a screw in the back for adjusting the set voltage. If that is an ASC from the 1990s, you could do a useful upgrade to a better controller for under $75.
It is not the wattage of the panels that counts for how many cells it has. There can be 50w 33s and 50w 36s. To get proper charging voltages in the high 14s, it is better to have 36s.
EDIT-Missed the bit about the pump labouring when the monitor showed red for low battery. Also confused about the "charging light" which is the one in the ASC??? Not the monitor's light???
Anyway, check the actual battery voltage at the battery compared with the monitor's light. You could even have a good battery voltage at the battery, but low voltage inside the rig--use your meter a the Dc fuse panel where battery wires come in and elsewhere such as inverter input, a DC lamp, etc. Might be a loose connection somewhere, or water in the porch light, all sorts of possibles.
