I have never had a problem booking a ticket over the phone which could not be booked online by simply feeding the agent the exact itinerary, along with dates and flight numbers, so long as what I want to do is "legal."

I have had agents point out that what I want is doable, but appears to add vastly to the ticket cost and then ask whether I am certain that I want to do what I've asked for.

There has to be more to this story than what OP has said.