When a Pokémon with Pressure is targeted by a foe's move, one additional PP is deducted upon execution.
Your attack has to have targeted Spiritomb for Pressure to take effect, because Swords Dance is not directed at Spiritomb, your Aegislash did not lose 1 extra PP.
Edit: You may have not been paying careful attention, and misread the game, believing your Aegislash lost only 1 PP.
If you are completely sure that Aegislash only lost 1 PP, then it is most likely a glitch. It is not in the List of Glitches in X and Y, so is probably a minor one-time glitch, and is not likely to happen again.
Another possibility is a change in game mechanics, for example Ghost types are immune to Grudge, but this is extremely unlikely, as X and Y have been out for almost a year now, and would have been found, I only put this down as a possibility because there is a (very)small chance this is the case.