I had a bike fit a few years ago (Qualified physio, PhD, lecturers at Uni and publishes papers on these kinds of things). Had a bike fit I was comfortable with for a few years.
Got my new bike - got sore knees, so tried to be loyal to my lbs - Did a brand name bike fit that put my cleats really wide (partially due to hip issues) & wanted me to purchase speedplay with long axles. Never got around to speedplay as I was relatively comfortable on my cheapy MTB pedals.
It never seemed right though going wider.
After 12 months I had sore knees again.
Went back to the original bike fitter who did the exact opposite with the cleats - as narrow as possible and my knees are much happier. Also my particular hip issue doesn’t mean I need to go wider with stance to fix it.
So… it’s a case of deciding who to trust with your bike fit I guess?
To the OP though - I guess the take-away I had was that if it feels like your knees aren’t being pulled in the right direction when you pedal then they’re probably not.