Not at checkout, but I'm continually frustrated by the default search results on DL.com not showing the lowest priced options for connecting flights.

For example, going BOS-MCO via ATL. A BOS-MCO through fare in Q might price at $300, but search results will give you BOS-ATL in L and then ATL-MCO in U for a total of $350.

For one-way flights, you can see this and use the fare class option to force it "up" into Q class, but that's an annoying waste of time and also impossible to do when you want to book a RT or multi-city on one ticket.