Originally Posted by ITA Hacker

In general there are thousands (and sometimes millions) of valid prices for any given itinerary. Our intent is to return the lowest one. If the system is returning anything other than the lowest then we're not choosing it based on any particular principle. The second lowest is usually not very interesting, as it's usually just a few dollars higher and doesn't provide any additional benefits (e.g. by being in a different fare family or even booking class).