Well. There are probably about 1000 answers to that question. Sometimes parallel squats are better. Sometimes below parallel squats are better.
Doing the same type of squat all the time will cause problems for anyone. That is just how things work. Rotating exercises is always a good idea. Even small changes can make a difference. Different width stances, pushing through your heels more, pushing through the "middle of the foot" more are some good variations.
You may learn what is better for you trying some different things.
Only gross mistakes can be seen on a video. You need to have someone who knows what they are doing look at you in real life.
A lot of guys get issues with their knees with squats simply because they do not understand the finer points. There is a lot to learn.
Personally, regular squats cause me problems if I do them too often. I work in box squats a lot in order to keep stress off the knee. There is a big difference in the box squat and free squat. Everyone is different, that is what has worked for me.
Another thing that can "assist" knee issues with the squat is very week hamstrings compared to the quads. Just in case you think your hamstrings are comparatively strong enough, they are not, and exercises need to be done to make them stronger.
A lot of people think that the hamstring can be properly trained with RDL and other hip oriented exercises, the truth is that knee flexion exercises are necessary as well.
I know this post does not have an answer to your question. But I hope it helps steer you in the right direction.