Realistically if there is an error its fully possible that the booking would look like something else has happened like a schedule change or other issue. It takes maybe a few minutes to look at the ticket,the itinerary history and the flights currently in the pnr to try and build an accurate picture of what has happened. Its not surprising they might think it was a couple of different things before finding the correct reason. Also they werent just rigidly sticking with one opinion, its like “i think it might be this” but they checked and investigated further.I dont know why its so terrible the agent didnt figure it out instantly!