TwiZtah said:
If you do squats slightly wrong, your ankles and legs will fuck up, hire someone who knows how to do squats the right way. Also, do some swimming, it's good training and is extremely easy on joints.
I don't think that's it though. I keep my knees parallel to my toes, make sure to hold a correct posture, and never bring my ass below my knees.
I've always had trouble with my ankles, long before ever doing my first squat. I would scream bloody murder at my mother when she tried to take me for a jog, and that was at age 9. Probably should have consulted a physician at some point, but I was a fat, fat kid. Back then I just assumed that my legs were hurting because of that, so I never made a big deal of it.