Depends. Is the motor plugged into the controller? And bolted to the frame? Or is it disconnected from everything and separated from the frame?
If the latter, then no, it shouldn't do that; it probably means that either a phase wire thru the axle has been damaged (usually at the axle exit) and is shorting to the axle itself, or a winding is shorting to the stator laminations.
If the problem did not exist before the bearing replacement, then axle wiring is the most likely culprit, as it could be damaged during cover removal or reinstall.
To find out *which* phase it is on, you would need to disconnect the Wye point between the phase windings inside the motor itself. Then each phase is independent and the short would only show up on the actual damaged phase.
To see whether it is a winding or phase wire problem, you would have to disconnect the winding from the phase wire, and test each. The one that's still shorted is where the fault is.
If the former, then it could do that if the battery negative wiring of hte controller is grounded to the frame, and the axle is grounded to the frame, and the test equipment's continuity / diode mode is capable of causing the FETs in the controller to conduct during the test, so that it's really seeing the battery negative conection thru the FETs, not a short in the motor.