Initially I was thinking, "There must not be 3 left in the cheaper inventory." However, since you said you booked the 3 separately at the cheaper price, that's not the case. I wonder if there were indeed less than 3 in the cheaper inventory, but in booking individually, the systems didn't sync quickly and you managed to snag the cheaper fares anyway?

Incidentally, I've on rare occasions seen the opposite: booking 2 pax resulted in a slightly cheaper fare per pax (on the order of $25) than had they been booked individually. I have no explanation at all for how that works.