Here's my understanding;
Book canon-
-Crichton intended the park raptor to be what we now call Deinonychus, but he wrote the story providing a mystery that left the question open for debate.
-Dr Wu, working for InGen, extracts DNA from an amber found in Mongolia. They can't know what they have until they hatch the first clone. Even then, they don't know exactly what they have because specific species might not have left any fossils. So they intended to rely on Paleontologist to look at their clones and tell them what they have based on the fossil record. Velociraptor mogoliensis comes from Mongolia, but what hatched was way too big to be Velociraptor mongoliensis. Was it something new or that didn't happen to be preserved in the fossil record?
-Dr. Grant is a paleontologist and a leading expert on Dromeosauridae, the new [Deinonychus] antirrhopus especially. The Park's raptor is clearly [Deinonychus] antyrrophus, but one thing confuses even him: [Deinonychus] has only been found in the U.S., and none have yet been found in asia at all. Maybe a third species in the Velociraptor family? Or maybe we haven't been looking hard enough in Mongolia? Either way, Grant finds it fascinating.
Movie canon-
-Speilburg was friends with Crichton and wanted to stick to the science side of sci-fi, but by then antirrophus had been reclassfied into a new genus: "Deinonychus." Hollywood happened, and it was decided "Velociraptor" would sell better than "Deinonychus." So the films (and every game) has called them Velociraptors.
-Dr. Grant is introduced somewhere in the western US digging up a large dromeosaur he calls "Velociraptor".
-Dr. Wu and the InGen lab techs seem to know what they're growing, and if they have any doubts they don't share or discuss them with the tour group, and evidently saw no need to consult a leading expert on the animals like Dr. Grant (the Entertainment division simply wanted his endorsement for the brochure).
My own head canon (which I've had for a while): 3 animals
-Deinonychus antirrophus ("Counter-balancing Terrible Claw"): Found in USA. Doom turkey stands about waist/belly-button height.
-Velociraptor mongoliensis ("Mongolian Swift Seizer"): Found in Mongolia and northern China. Psycho chicken stands a little above the knee.
-Velociraptor hammondi ("Hammond's Swift Seizer"): Found in Mongolia and northern China. Movie monster stands about shoulder height, but the films want you to be intimidated by it so you rarely get a good shot where full grown men aren't looking up to them; they're almost always crouched, hunched, or straight up getting pounced on. Also, I don't know who started calling it "hammondi", but I love the name.