They most likely did raise this, but when asked to provide a more "competitive" bid, they axed training and who knows what else. This is common in large enterprise sales deals. For professional services deployment engagements, there is always the possibility of an amendment to the services scope (often referred to as a change order or change request).

If the project is estimated to take over a year to deploy, by then you're in a new budget cycle and the vendor has come to an agreement with the procurement department to charge for additional services as required in subsequent phases.