Hi and
to the forum.
As you haven't mentioned which motor you are using I will assume that it is most likely a minimotor.
The only voltage you should see on the controller's motor wiring with the motor disconnected is the +5V feed to the Hall Sensors which can be measured between the Red and Black wires on the Hall Sensor connector.
I wouldn't recommend applying battery voltage to the Blue and Yellow Phase wires as the current will be very high and is likely to produce a big spark and could overheat the Phase windings if left connected for too long.
It is better to measure the resistance between each pair of Phase Wires in turn
(Between Yellow & Green, Green & Blue and Blue & Yellow) to confirm that all of the three readings are very similar.
Alternatively, with the motor disconnected from the controller try touching together each Phase Wire Pair in turn while turning the wheel backwards. If the Phase windings are good, the wheel should be difficult to turn backwards manually while each of the three pairs of Phase Wires are touched together.
If the Phase Windings check out OK and are all the same, it may be a Hall Sensor problem.
Unfortunately, the minimotors will not run in sensorless mode because the motor needs to be turning so that the controller can detect the movement, but the internal freewheel mechanism
(unidirectional clutch) prevents this from happening.
Take a look at
this post and
this video for information on testing the operation of the Hall Sensors.
With a minimotor, you will have to turn the wheel backwards while testing the Hall Sensors as the unidirectional clutch prevents the wheel from turning the motor in the forward direction.
If a minimotor has been overloaded for too long it can overheat, causing the insulation on the Hall Sensor wires to become damaged due to excessive heat build up in the motor windings:
When the insulation melts, it allows the inner copper wires to short circuit.
Alan 
