Did the swelling involve the entire fetlock? Or was the swelling in small spots above, or below, or on the fetlock? If the entire fetlock was swollen I believe it probably is in fact that she was stocked up, especially that the swelling went down with exercise. No lameness though, when she moved? Probably a little stiffness I'm sure. If it is possible ensure that she gets plenty of turnout. It is pretty common to see with horses that are exercised then put into a stall after. Also be sure to provide a good cool down period, and consider doing some leg stretches before and after you ride.
However, if the swelling is in small soft spots above, below, or on the fetlock that are soft to the touch with little to no marked heat it is possible that they are "wind puffs", also called "wind galls". These are soft "spongy" swellings around the back, front and or side of the fetlock joint. Internally the joint capsule becomes enlarged with additional joint fluid in an effort to protect it against injury. Typically they are caused by joint concussion, excessive work while the horse is young or out of shape, or general stress & fatigue of a heavy workout on the joints. Unfortunately with wind puffs they never go away, but they don't seem to cause any dramatic lameness as long as the joints aren't continually stressed.