The other question I'm wondering would be, how could it be possible in that case that A -> B directly would be more expensive than A -> B ->C ?
Of course, the second flight probably isn't 100% sold out, and you might have gone with a competitor or not taken the trip at a higher price. But they don't necessarily see that, much like music labels don't necessarily understand that every instance of piracy is not a lost sale.
First, you probably shouldn't do this as the first part of a roundtrip ticket, as the airline can cancel your return if they think you're abusing the system. That may not be important for many people, but it's there.
Second, if something goes wrong (bad weather, can't find a pilot, whatever) the airline may reroute you through a different city, completely screwing up your plan. They don't really care where you connect, and as far as they know neither do you. If you book, say, JFK->LAX->SFO and the engine falls off your JFK->LAX plane while sitting at the gate, they might move you to a route like JFK->ORD->SFO, and saying, "but, but, I was going to leave the airport at LAX and skip my flight to SFO" is probably not going to get much sympathy from the agent.
A note on the roundtrip booking - correct, you should never book roundtrip. Your roundtrip should be made up from two one-way bookings.
the overhead compartments are full and you have to check your bag.