Started cycling to work, 14 km each way. Knees hurt after week two. Normal?

Bought a hybrid bike in August and started cycling from Dwarka to Gurgaon three days a week. Loved it for the first two weeks. Then a dull ache started in both knees, worse going up flyovers, and now I feel it even on the stairs. Seat height is set so my leg is almost straight at the bottom. I am not pushing hard gears, or I don't think I am. I did not do any warm-up because it is a commute, not a workout. Cyclists here, is this the usual beginner thing that settles down, or a sign my setup is wrong? I do not want to stop but I also do not want to be that guy who wrecked his knees at 29.