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Are you hips out of alignment?
You may need a hip adjustment from a chiro.
Have you had a coach or training partner what you squat or video tape yourself squatting so you can see exactly what is going on.
When you get use to doing a skill with deviations from ideal technique doing it with proper technique will seem weird. Breaking any habit is tough, however, keep working with it.
What is your hip and ankle mobility like?
Squat Quick Test: Is it Tight Ankles or Tight Hips? | Community Video