To be fair to the BBC, I would imagine that the 3 O clock kick off games were in the process of being edited and being in the can before the Burnley v City game finished and the late kick off meant that the other games had been edited and put into the programme already.
Having said that, I'm not sure whether that is actually the case, as I don't always watch MOTD or if I do I usually just Sky plus it and fast forward to City. Whether the other late games take a lower billing (if that's the way you see it) I'm not sure.