I would also suggest looking at her lunge form from a frontal view. If she pronates in the foot her knee may be caving inward causing problems. I like to cue “pressing through the heel” of the front foot to encourage more stability. Another exercise you could try is squats with a stability ball behind the back (full range or half). I feel that the client can get the 90 degree bend that they get in the lunge. If she can do this with no tweak, you can challenge her with a single leg ball squat as well.
Hope you two can find a solution!
Take a look at the relationship between her knee and ankle, her knee should not extend over her ankle joint and her hips should not go lower than her knee joint.
If that doesn’t help her, I suggest having her not go as low as she has been OR have her do mini squats while others do lunges.
If the squats bother her knees have her step up and down on a platform or bench or curb while others are doing lunges
I hope this helps