Are you doing feet at shoulder width squats? If so knock that shit off.
You need to be doing wide stance powerlifting style squats and box squats. Nothing will shoot up your hip flexor and glues like that shit. Not to mention your deadlift will automatically go up by default.
Youtube louie simmons and watch his squatting vids.
Louie Simmons On Wide Stance Squatting.wmv - YouTube