It is hard to give you a specific answer without looking at the model.
I believe you are applying a discrete motion signal, which will move the joint in steps. Each time the joint makes a step change, you will see a spike in the applied torque (or constraint torque). If you were able to simulate this as a variable step simulation and you can ensure that the signals are not applied in discrete steps, you would see values that make more sense to you.
--Steve
