Booking your flights with Disney is not as bad as booking with Expedia or Orbitz but would be worse if you can't confirm your flight times.
Airlines cancel flights often, forcing travelers to be rebooked. Dealing directly with the airline makes it much easier for you to be on your toes and reselect flights quickly.
Sorry but the above is too late for you. Would email work better than the telephone for you? Costs can rise unexpectedly, suddenly, and rapidly if you run out of anytime minutes.
I don't know whether Travelocity or
AAA or Disney do it but some travel agencies prepurchase blocks of seats, rooms, etc. at a discount. Should your flight be cancelled, the agent wants to give you another seat out of their allotment. If you hand pick a flight that the agent has none of, the agency would have to go "outside the box" and buy it for you, and worry later about selling the seats still in its allotment. So the agent either grumbles to himself and/or gives you a hard time.
More likely the answer is that their software engineers neglected to include a space in your reservation details page to show the confirmation number. Too many times I get a bill or statement and, after I tear off the top to send with my payment, the part I have lacks the billing address, the condominium unit number, or something as basic as that.