The brontosaurus -- the most famous of all dinosaurs, the emblem for Sinclair gas and the model for the Flintstone's Dino -- never existed. O.C. Marsh somehow got some head's mixed up and what he thought was a new type of lizard was really just the previously discovered apatosaurus. Thus we call the animal the apatosaurus today, yes. The animal existed. Does the species we call "dog" exist, or is it just what the Romans used to call "canis?"
The answer is "yes." It's not and either-or question.
Marsh thought the brontosaurus was a differnt type of lizard than the apatosaurus. The apatosaurus existed when he found what he thought was the brontosaurus. It's more like calling the fossil of a horse a unicorn because it's skull got mixed up with one from a rhino.