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It has been Apatosaurus since the 1890s, but they also "discovered" another related species at the same time, which was named Brontosaurus. In or around the 1970s, it was confirmed that Brontosaurus never existed and was a result of the skull of a random other dinosaur getting mixed in with an Apatosaurus skeleton. This isn't like Pluto.
The head thing was a separate incident from the Apatosaurus/Brontosaurus confusion. For a long time they didn't know what the head of the animal looked like since they never found one attached. It was thought that it was related to Camarasaurus, so they just used a Camarasaurus skull instead. This is actually not uncommon, since complete skeletons of dinosaurs this large are rare. The proper skull was actually found in 1899 a short distance from the specimen found for the Carnegie Museum in Pittsburgh, but it was thought to be too small until further studies in the 1970s showed that it was the proper head. Apatosaurus is actually more closely related to Diplodocus than Camarasaurus.
The Brontosaurus story is a lot less interesting. In 1877, OC Marsh discovered a large sauropod that he called Apatosaurus. In 1879, he found a larger sauropod he called Brontosaurus. This was the time period of the Bone Wars and the discoveries were described poorly with the intention of finding as many new kind of dinosaurs as possible. In 1903, it was determined that the two specimens were similar enough to be the same genus, and Apatosaurus would take priority because that was the name given first.