How low are you squatting ? Since you mention there is no pain at all, I don't think this is an alarming issue.
Usually the popping sound in the knee can be related to the synovial fluid present in the synovial cavity.
Check this pic to understand more:
The synovial fluid gets filled with bubbles of air and they cause this sound when doing movements or bends such as squats.
Now if you feeling something is cracking or moving inside, then it is better to get your knee checked by a doctor or physio.
In the mean time, make sure to warm up before squatting.