I think the main reasons some people are bothered by this Deinonychus is that it exemplifies just how carefully Frontier had to tread to avoid messing with the lore. They wanted another raptor in the game, and Deinonychus is the most recognizable name. But the original JP Velociraptors are "V. antirrhopus," because at the time of the novel the placement of the genera was uncertain. By the time the movie came out, it was known that Deinonychus and Velociraptor were different things, but apparently it was a creative decision to name the animals Velociraptor, even though they were based on Deinonychus. So Frontier goes to add Deinonychus, but they can't, because that's what the (already wonky) JP raptors already are, so they have to make their Deinonychus even weirder.
I don't get it-- if Frontier has some creative leeway when making dinosaurs that haven't previously been featured in Jurassic franchise media, why didn't they just make Deinonychus a scaled version of the real thing? It would be smaller than Velociraptor and clearly much more gracile than the JP raptors. I assume they didn't pursue this route because all of the ancilliary material in the game describes the dinosaurs through our current understanding of them, like how Metriacanthosaurus is placed within its own group (the original JP Metriacanthosaurus was likely meant to be Yangchuanosaurus), or how Nodosaurus reflects the coloration we know Borealopelta had. So they couldn't portray Deinonychus at its accurate size, because the flavor text probably needed to address that it's related to the smaller Velociraptor.