I've seen this a few times. Usually in the Admiral's Club rather than at the ticket counter (because that's usually where I go when I have a problem), and usually because of "Irregular Operations" (flights delayed and potential mis-connects).

I think that the official rule is that they are not allowed to put you on the non-stop unless there is going to be a misconnect, but this seems to allow them the flexibility to change it for you if you are nice to them.