According to the Wikiepedia article on Deinonychus,
Deinonychus were featured prominently in the 1990 and 1995 novels Jurassic Park and The Lost World by Michael Crichton and the film adaptations, directed by Steven Spielberg. However, Crichton and Spielberg ultimately chose to use the name Velociraptor for these dinosaurs, rather than Deinonychus. Crichton had met with John Ostrom several times during the writing process to discuss details of the possible range of behaviors and life appearance of Deinonychus. Crichton at one point apologetically told Ostrom that he had decided to use the name Velociraptor in place of Deinonychus for his book, because he felt the former name was "more dramatic".
The world of Jurassic Park is filled with prominent, respected and intelligent paleontologists, botanists, geneticists and historians. Yet despite all of this, they all call the tall scary dinosaurs Velociraptor, instead of Deinonychus, as they are known in the real world.
In Jurassic World, this is sort of addressed when Claire says of Indominous rex:
"We needed something scary and easy to pronounce. You should hear a four year old try to say 'Archaeornithomimus'."
Out-of-universe, Deinonychus was chosen because it looks scary, and the name "Velociraptor" was chosen because it sounds scary. But both of these creatures exist in the real world — the latter being much like an angry naked chicken.
In-universe however, has there ever been an explanation for the name swap?