In the video I can see you are doing the butt wink, basically you curve your butt inwards at the end of the squat, your butt and hips shouldn't move other than up and down, which is a common mistake. I have no advice on how to fix it, because I am not a fitness instructor, but you can google it and find some solutions. 1/2
2/2 what helped me with my knee problems was doing squats extra slowly and more controlled with lower weights, so I built up my muscles enough to stabilise my knees while doing the movements and now I can go lower without hurting my knees. I ignored the pain in my knee ligaments before that, until I ended up spraining my knee and having to stop working out for a month, so yeah, try not to do that :D
Thanks. I'm aware of the butt wink, I have been for some time, I'm just not really sure how to fix it, though @iversays has given me a few things to try. I spent quite a long time squatting controlled at lower weights. My legs are plenty strong and my knees don't hurt while squatting, it is in the following days that they ache. What a lot of people have suggested and what I agree with based on how stiff I am, is that it is IT band related due to stiffness. I'm going to be working on doing lots of foam rolling and stretching to help the muscles ease up, as well as lengthening the amount of time I spend doing a cardio warm up and adding a cardio warm down prior to stretching. Thank you very much for pointing it out and for your advice, anon.