I'm still a crossfit beginner but have been lifting weights for 20 years.
Squatting has always been a problem for me due to biomechanical issues (long back, long thigh, wide pelvis, short shin, rigid ankle joints). I cannot balance unless I use a really wide stance and lean forward a lot. For this reason, I always used to squat in a Smith Machine where I could shunt my feet forward and lean back into the bar. But for regular squats, I'm crap.
Now I'm in older and work a sedentary job, my hip flexors have got very right, and my knees hurt a lot (that's more to do a problem I got running on pavements).
Deadlifts have never caused me too many problems though I've always preferred to do Romanion (stiff-leg) lifts in the past - I guess I just don't like bending my legs too much.