There are a lot of factors that can cause knee pains.
for hip pain, it's usually the saddle being too high.


Things that can cause knee pain
imbalanced leg muscles
q-factor too wide
crank length too long
saddle height too low
low cadence
bad cleat placement
uneven feet soles, correctable by angled cleat wedges.

As far as Q-factor goes, for shimano triple it is about 155mm, and for double it is about 142mm.

have your wife cycle on regular platforms with the running shoes and special inserts. See if that helps.

For me, I only get knee pain if the saddle is too low and the Q-factor is too wide with clipless. On platforms, I can place my feet in closer to the crank, which makes Q-factor, effectively, narrower.