Can't say I've ever specifically had pain there from squatting. But I find that with squatting more so than other exercise from one session to another your body can become sensitive in different areas. I use the same form each time and can have sessions I come away from feeling entirely fine, however other times I've felt pain in my knees, calf, ankle etc.
I find that if something hurts, immediately stopping and not doing squatting for a week or so until the pain is not only gone but the area feels strong again, is the best thing you can do.
You don't want to push for short term gain at the expense of your body in the long term.
Make sure your feet are shoulder width apart and your back is straight, if you've got those in mind with squatting it's hard to go wrong.