If you used the TA I think you did, they book you as "convention" which is how they get lower ticket prices and hold a block of rooms that can be sold at lower prices. In
MDE my reservation made with this TA says convention. The concierge probably saw it in the system and asked. Curious how you responded?
Who put the $900 charge on your card? Disney or the TA? If the TA did it because they only do standard view and the hotel gave you garden that is deeply worrying because it is an unauthorized charge and it means she was spying on you. If Disney did it because they felt your reservation was a lie when you said you weren't at a convention, that is almost as troubling because they don't have the right to just charge you with no warning. In either case if you were given something you didn't ask for and not informed it was yours at an addiitonal charge, you can dispute it and I so would.
Personally I hate that they stopped the paper bill under the door before departure and email you after you leave. It allows for stuff to go unnoticed until too late. I charged direct to my card, never through a mb, so I don't think to stop at the desk or check online because I know what I put on it and pay cash for meals so there are no random over tipping "accidents" but after this I think I will pay a bit more attention.
Side note, but I used this TA for the price and have found using a TA such a hassle compared to doing it myself I doubt I ever will again. If this charge of yours is because of TA spying to see you were upgraded or because Disney caught wise to the convention trick it is certainly not worth the discount.