We have the same problem but I don't stand for it at all.

Recently was travelling from London to Kuala Lumpur, Malaysia. Agent said "there are 3 Malaysian Airlines flights, leaving London at 1200, 1800 or 2200, which do you want", to which my reply was "the 1800 stops at Penang and is overtaken by the 2200, so why ever would I want that one?". Reply: "Um.... oh yes". And as a result of similar happenings I am known as a "nuisance" by the travel agency staff. But when the contract comes up for renewal, such issues are one of our prime grounds to change travel agent. Which we have done twice in recent years. And in the meantime tell them to rebook you properly, especially if they are giving away your personal time to save the company money.