If you input too fast on extinguishing Soul Vessels when you've extinguished it already, you'll lose the extra AP you spent. Additional AP spent is lost when you re-extinguish during the animation of it turning off.
For example: A Soul Vessel has 10 HP (needs 1 action/2AP to extinguish), you input the extinguish once, then another time during the animation where the Soul Vessel is getting extinguished, you'll spend the first 2AP to extinguish, then another 2AP because you inputted mid-animation, resulting in you losing the extra 2AP.