I use Agoda as my go to OTA when I do not book direct and find them to be excellent. Hotel always has my reservation, prices are honored.

As to your specific complaint, this happens. They are obv a marketing organization. Were you only booking the room because it was the "last one"? Why would this make you book? Perhaps Agoda only had 1 room remaining, and then got more inventory from the hotel. Sometimes the OTAs pre-buy inventory, they aren't just showing what is or is not avail from the hotels inventory. I'm struggling to understand how their marketing hurt you. It may mislead, but you booked a room at what you felt was a fair price and if they delivered on that - you were served.