That's an odd one isn't it - they weren't checking things very carefully when you specifically asked what model it was.
That wouldn't bother me as such, but as you rightly say, as and when you come to sell it, you'd need to advertise it as an upgraded 9.0 rather than a stock 9.9.
Only you know how much of an issue that might be, and no one knows how much money (if anything) that could potentially cause you to lose on a sale.
I'd be inclined to drop them a friendly message stating that overall you are content with the bike, but the fact that you asked a specific questions about which model it was, and another one being stamped clearly on the top tube is a bit of an issue, and I'd reference the potential resale issue of it not being a stock model.
I'd not suggest a remedy, I'd be inclined to say this is the issue, is there we anything you can do to remedy the situation, and see what they come back with.
This is not the same as such, but pre ashley I bought 3 bikes from
Evans.
I won't bore you with the horribly damaged one, but basically 2 of them came with incorrect parts, ie one had an alloy seatpost when it was clearly specced with a carbon one, and in fact thinking about it, it was an identical situation for the other one too. Both were Dales.
Happily I spotted this (I wonder how many people do not) and contacted them to point out the errors, one they sent out a new post, another one I sourced it and they refunded me for the amount once I provided proof of purchase as they had no stock.
Your situation is clearly different, being a used bike, but the fact remains that the model stamped on the frame is not what you thought, and were critically told, you were buying.
It's worth an ask at least.