The DC-DC module may be doing its current measurement on the 'low side'. In other words: inside the module a small shunt resistor for measuring current may exist between the negative output terminal and ground.
EDIT: When you say that the negative output terminal is connected to ground, how did you measure this? Did you follow the traces or use a DMM? If the latter then there might still be a small shunt resistor there (less than a few ohms) OR an entire low-side switching mosfet that was 'on' at the time of measurement.
It would be cheaper/simpler to low-side switch, even though it has some disadvantages, so they may have done that.