I will assume you to mean ...

I will assume you to mean that you have two flow sensors on the same line, one after the pump and one on discharge to the reservoir, magnetic type. Will mention the basics.

Apart from the obvious regarding calibration (which depending on the quality of build, can be in-situ or has to be removed and calibrated), flow meters are most accurate if installed in as straight a pipe run as possible (15 x ID in length before and >5 x DI after) to dampen a turbulent flow with nil air and at a respectable velocity (>1 m/s minimum, 3 to 5 m/s preferred). Which of the two locations better fits the above is the one i would trust more.

Pump stations are typically housed and therefore tend to be compact in installation, including the attainable straight run of pipe. The pump station piping tends also be larger to account for downstream pipe friction which then affects the measured velocity, and therefore the accuracy.

In this situation the flow sensor is better installed in a reduced ID section of pipe which helps to stabilize the flow, shortens the foot print, reduces instrument cost whilst increasing reading accuracy.