The static ability of Phantom Centaur, which should only activate when it takes damange, still activates even when a damage prevention effect is used.

The card Phantom Centaur (https://scryfall.com/card/jud/127/phantom-centaur) has the static ability "If damage would be dealt to Phantom Centaur, prevent that damage. Remove a +1/+1 counter from Phantom Centaur."

The card Hypochondria (https://scryfall.com/card/tor/7/hypochondria) has the activated ability "{W}, Discard a card: Prevent the next 3 damage that would be dealt to any target this turn."

If the damage prevention effect of Hypochondria is used on Phantom Centaur and then Phantom Centaur takes 3 or less damage the game prompts for which effect resolves first but regardless of how the effects are ordered a +1/+1 counter is removed from Phantom Centaur.