That's exactly how its supposed to work, the current waveform should be roughly an asymmetrical triangle wave. To reduce the amplitude of the current variation you can use a higher PWM frequency.
You need to be aware that the current shunt should be sampled in synchrony with the PWM for stablest behaviour. Or you can low-pass filter the current shunt signal (this will affect any control loop though, which might have to become slower to respond.)