Can present value of Iq go to negative for a positive value of Iq reference

I am giving a reference Iq of around 600 in terms of number which corresponds to around 2A based on internal calculations. But i am observing that the current Iq goes to negative value of more than 1000 that is -1200. My question is can the current Iq and Id go to negative values? I am asking as there is invalid switching in between the sectors.