If you're worried or getting caught up on the "order of events" or continuity idea of it (like stopping to attack mid-overrun), remember that rules used to *play* pathfinder are just our best effort at what is, in the theater of the mind, a continuous, fluid fight. Feats and abilities are distinct, unique ways to improve your character and what they're able to do, not lock you into a box of the only three things your character can do in combat and what order they can be sequentially accomplished in.
Yes, per the feat you did not trigger the AoO until the creature was knocked prone, but all that is is our best effort to build your character's unique ability to have the chance to *both* be able to combat maneuver *and* do damage. There is absolutely no requirement that logic-wise or story/theater-wise that's how that action went. Maybe your "overrun" of the creature was smacking it upside the skull with a mace, which resulted in the creature both being knocked prone and taking damage, and you're on your merry way. And maybe if you miss the AoO, instead of you hitting the target, it tried to dodge your mace swing and tripped and fell over, or even willingly dove itself to the ground. Combat in pathfinder does not have to be A > B > C > D > E and so on. The rules and logic of feats/abilities are just there to set a standard and maintain consistency/fairness, not to tell the sequence of events for you.
This is coming from your friendly neighborhood Slashing Grace, Greater Trip Hamstring-severing Swashbuckler
