It can happen on Longhaul too. I had to change the dates of my flight to HKG a few years back, at somewhat short notice. I'd been booked to go out in J (as is usual) but when I had a quick look at new times and dates before sending preferences to the team PA, I saw that on my preferred flight, F was cheaper than J, albeit with ba.com showing "1 remaining seat available".
Needless to say I finished typing and sending out that preferences email pretty quickly and the outbound selection was in bold with a very large font.
That one seemed very odd to me. Didn't think it was part of that 'book J, fly F one leg' travel agent promotion that they run occasionally. it just looked like a wierdly cheap ticket. Certainly nothing wrong with the service. Was new F on the A380.