Yup- check your form- are your knees going past your toes when you at the lowest position? If so- you're putting too much pressure on your knees.
excellent avatar; good advice.
this is something I had to change, too. I was doing squats and my knee kept hurting (though I blame it on poor footwork in Muay Thai--working on that). I changed form so my knees don't go past my toes and it's lightened up.
I won't mention that it was my girlfriend who corrected me.