I'm really sorry for your misunderstanding. It doesn't sound like the person had any intention to deceive you though, they just assumed that you knew "buying" a house meant that you are paying them to relinquish the land.
I think this really ought to serve as a warning to sellers to make sure that the buyers they find are actually able to afford the land and understand what it is that they're buying. But at least understand that relinquishing their land for 3 million was already a huge deficit to them, so expecting them to refund your gil because of your mistake is problematic.
This is kind of a lose/lose situation that arose from a misunderstanding, not a scam. The only proper way to fix it would be to give the sellers their land back and give you your money back, which hopefully SE can do.