When truing wheels, I go gradually. Turn the wheel to a spot where it is out of true (rim rubs against the truing stand indicators), make at a 1/4 turn (in the appropriate direction) in the nipples at that location, then - whether the rim is true or not - move to the next trouble spot. Keep going around and around. Little by little, get the rim true. Eventually go to 1/8 turns.

Also, I try to spread the larger adjustments over a few spokes. Not just tighten this one spoke, but also loosen the neighboring spokes on the other side, a little. That helps avoid creating low spots .

If you're willing to find "The Bicycle Wheel", it explains all of this in a clear, short book .