I've experienced it myself searching on United.com. But yes, sticking with a single airline's usually a good idea — there are benefits towards acquiring elite status on a single airline's frequent flyer program (even when we're talking about airline alliances).
I usually use ITA Matrix > Expedia (which uses the engine, I think) > Orbitz (if it has more segments than Expedia can handle — this also uses ITA's engine).
For low-cost/budget flights around Southeast Asia, I just use Skyscanner.
$507 vs $528, and both have Pegasus where Momondo shows the cheapest Pegasus at $507 and Hipmunk at $553
and a self-quote from an email conversation I had in december about flight search engines: "Just to picture an example,
random query 30dec-05jan Warsaw-Istanbul. Hipmunk cheapest: 407usd (turkish). Momondo cheapest: 299usd (aerosvit). that's over 1/3 more."
Frequent travelers are generally best served by sticking with a single airline.