I think Edward has the right track... I have a torn meniscus in one knee (from college crew) and it occasionally acts up during Aikido, but it also occasionally acts up when I run, or on long marches. Nothing in Aikido has hurt the other knee. I think when most complain about knee problems, it is just old problems we have brought to Aikido.
I think there are two things, if done incorrectly, could hurt you in Aikido: tenkan movements if you 'plant' your foot and try to turn on it, and surari waza/shikko if you put you weight over your knees, or bang them down, or don't keep your heels together. But done correctly, I think there is no stress on the knees.