One way to take a quick look is to video yourself from the front squatting with the band and without the band. If your knee in both videos are tracking the same AND you’re not experiencing pain, then you’re doing the right thing! Just keep doing it!

I suspect you are having valgus collapse inward on one leg which is causing your knee problem during the squat. During a heavy squat you may not even notice it in the heat of pushing the weight up. But you notice it after with the knee pain.

So yes your movement pattern on the squat is faulty which means some sequence of muscle firing is not right.

Movement patterns are wonky.  Just because it happens here doesn’t mean it would happen in another movement.  There are other correctives which address valgus collapse but they are for other movement patterns which may or may not translate.  So mobilize mobilitywod style to make sure you have no restrictions in ROM which may be causing the problem, and keep using the band RNT and slowly wean yourself off of it.  Also, doing the RNT movement often helps repatterning – you may try using the band with air squats outside of your normal workout, just to keep imprinting the patterning.