Hey guys!! I have a question concerning a squat assessment :)

I'll try to keep this short!
My girlfriend has been doing crossfit for about three months now. She is an athlete, but mostly a runner, so she has very very strong legs. As you all know, deep squats are some of the primary movements in Crossfit (which I dislike because i NEVER make my clients squat that low with their knees turned out). My girlfriend told me the instructors keep telling her to squat lower and that her chest is falling forward. I told her to squat safely and that if she couldn't squat that low with proper form--dont do it!
I put her through a workout yesterday that involved body weight squats--knees/hips 90 degrees, knees and toes in line with each other. I was surprised to see even with no weight, he knees falling INWARD, LACK OF BALANCE, and CHEST FALLING FORWARD.
Now, in a squat assessment with a new, de-conditioned client, I would know the causes of these improper movements. BUT, as mentioned, my girlfriend has good balance, strong legs, and is an athlete. WHAT COULD BE THE CAUSE OF THIS???
ANYTHING WILL HELP! I just want to make sure she is doing these exercises correctly, and not becoming injured.