How dare I assume someone's gender, shame on me.
I was also speaking to the other exercises as well.
The point is, squats with good form aren't to blame for knee pain. Your knee issues are probably from over use without enough time for recovery.
You started by saying squats alone, then added you ran a lot, then heavy squats 3-4 days a week, then to top it off you stated the dreaded word "crossfit".
I applaud you for being healthy and staying fit, but sounds like an overuse issue and not a squat issue. Don't demonize the squats! That's how the terrorists win.