Perhaps the squats are causing tightness because you are loading your patella. Are you squating with your hips or your quads? Try squatting as if your sitting back with emphasize on glute/hamstring activation. Make sure youre knees dont come past your toes. Open up your hips during the squat as shown in some of the mobility wod videos. Then roll out your quads/IT band after the squats. Also maybe get some glute activation warm up before doing the squats, like clamshells or x-band walks or side lying leg raises against wall. This will help activate the glutes during the squats. 

Also if you can squat with a band around your knees this will emphasize the glute medius. The band will try pulling the knees in while you use your glute medius to push your knees out to prevent that from happening during the squat. Its essentially cueing those stabalizing muscles to prevent any knee collapse or valgus. 

Also, are you going parallel or below parallel. Have you seen a good physiotherapist or other health practitioner specializing in mobility and biomechanics that can fully assess your issue and if the squats are in a good form?