Is it bad to go past 90 degrees on my squat?
No, you should be going Ass To Grass (ATG).
Many people believe if you squat to a point where your legs have a 90 degree bend in them then that is low enough.
While that will stimulate and build the muscle, it will not be doing a total and thorough job. To get the maximum benefit from your squat, go ATG.
You will likely have to lower the weight you usually lift, it may HURT to start with, but you will achieve better activation. If you need to, place a mat under your heels to get squat all the way.
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