Skyscanner itself isn't cheaper and you *do not * book with it.
Skyscanner is an excellent research tool. If you book using the site then you are booking *through the agencies with which they work* e.g. Expedia.
It is important to be very clear about that aspect.
I use Skyscanner as a research tool and then book directly with the airline. I have always found the same fares on the airline's website that have been given on Skyscanner but I appreciate that this may very. I prefer to avoid third-party agencies when booking air tickets: too much can go wrong.
So you need to carefully check which Skyscanner-associated agency is offering you the 600USD fare.....and then check *very carefully indeed* exactly why there is such a price difference between (presumably) the same routing, date, airline etc.
I suspect that you have been quoted the fare for a one-way trip and not for a return trip, or there is a date variation. Unless you choose the 'whole month' option you will only see the fares for one particular day.
In my experience (I use it pretty much daily, several times a week at least) Skyscanner does list all mainstream airlines (and budget airlines) but their search facility is very specific in terms of date and, often, airports. Choose the 'wrong' date or the 'wrong' airport and an airline will not show...because it does not fly on that date or to/from that specific airport.
