Yes possibly as the Q factor (distance between pedals) is another of those things based on human averages. As we know, no human is average, as height, hip width, length of legs, arms, back etc can all affect ride comfort etc.
Try to look at all factors that make one bike comfy and ergonomic and another not then try to bring the bad one closer to the good one by various adjustments and unfortunately by even by changing parts. A Crank arm that does not bend out from the bottom bracket as much might reduce Q factor as long as it still clears the frame etc
Good luck, pain caused by a bike can ultimately sour the idea of that bike, so hopefully changes can be made.
EDIT: I had a few more wee thoughts to further explain Q factor and pains in knees.
If you look at an average human standing relaxed in front of you you notice that their feet are often closer together than the width of their hips, this is more pronounced in women who have wider hips. The Q factor on a bike determines by its pedal position the distance between one's feet, this position is often artificial as standing our feet may be closer together. The further our feet are apart from our individual relaxed norm the more strain however small is felt by muscles and tendons especially at anchor points situated at joints. As the Q factor of a fat bike that conforms to the Diamond frame classic design is significantly greater, then muscle and tendon strain is greater.
If Q factor cannot be reduced then a regime of muscle stretching exercises might be a solution if you want to keep riding the bike.
Some fat bike designs have got around the Q factor width issue by moving the chainstays up and out of the way via the e-stay method found on older mtb's. With the e-stays the cranks don't hit the chainstays if the Q factor is narrower and its even possible to use a standard 68mm BB shell. The original Surly Pugsley had an equally clever idea in that the rear hub which was standard 135mm was offset to the drive side with the wheel built undished. The chainstay stayed close to the tyre sides then bent outward to encompass the cassette. The result was the cranks could be less flared out as they were not in danger of hitting the stays and the Q factor could be kept reasonable. "Progress" however demanded the standard Diamond frame was proven strongest and wider but not standard hubs (chance to sell new expensive bits and bobs not wasted by marketing guys) was better and the result is your fabby fat bike