If after going to the toilet (doing number 2) one cleans himself with running water and no trace of najasah is left. But later during the day or the next day, one notices a very tiny color change on a tiny spot on the underwear. Would this be considered najis? Even if one was sure that everything was clean while washing?

If he is certain that the object is impurity, as if it had the smell of impurity, then it shall be judged as impurity.
As for doubt, and the possibility that the color is due to the remnants of water, it is judged to be pure