When I have to stop and put my feet down ( I hate when that happens
it hikes up my pant legs to where the pads are slightly not where they're supposed to be, causing discomfort after awhile. I will stand on the pegs, while still at slow speed, to shake my pants legs down where they need to be. This goes, too, with adjusting the knee pads positioning inside the pants. I found I had one more little notch of adjustment lower that helped quite a bit.
Someone else also touched on it - the rotation of your foot on the pegs. If I square up the ball of my foot on the peg, with the foot pointed forward, it does stress the knee and cause pain down the road. If I move the ball of my foot outward, alowing the heels to rotate in, it relieves most of that stress.
Also I'll move foot position fairly often. Ball, heel, middle, rotate in, rotate out. Variety is the spice of life.