It appears that the code which checks to see if you already know a mount cannot reference a flight form, which to my knowledge has never been sold at a vendor before.
During Legion there was some confusion by players who rolled druid to get “the mount” but didn’t get a mount. But I think the number must have been dwarfed by players who rolled druid because they wanted to play druid and eventually figured out how to access the shapeshift form.
As I said above, to avoid confusion I think Blizzard should create a utility to see if you have purchased this item previously on this character. And then not let you buy it again.