I've had this happen to me on a DCA-ORD-DCA flight. 2 passenger reservation gave price/passenger $x. 3 passenger reservation gave price/passenger $z>$x. I booked the 2 together at $x, and then one separately at $x. Because I was worried that booking the 2 together would wipe out a low fare inventory, I used two computers to simultaneously book both reservations.

The 'automatic replenishment' explanation works mechanistically, but seems strange conceptually. Is that a common feature of fare setting?