Episode 13 of Chuck in season 3 was clearly the intended finale to the show. It was odd to see the show climax, and then continue afterwards. Episode 14 seemed odd; unnecessary. Maybe the show was axed and then got funding for more episodes? Who knows?
Babylon 5 did the same thing. Season 4 ends wonderfully, and offers no scope for any real continuance, yet they scraped together fragments of material to produce a 5th lousy season which I have been advised not to watch.