Usually the logic in ecu's for relay controls are monitored to see if its low when it should be high (shorted) or if its high when it should be low (open) and throw a code based on that.
I have seen some logics dislike certain relays as well so maybe the system is monitoring more then just high/low signals and sensing current based on the relays coil resistance.
Hard to know much with out knowing the year/model. The ecu systems are quite different. It may not even be a control signal issue.