First, the whole thing about Indominus Rex. Yes, yes, I get the idea that they needed something bigger, badder, cooler, more impressive. With Jurassic World being some sort of one of a kind theme park and such, I would've thought it better to explain its creation primarily as a result of inGen attempting to weaponise dinosaurs. Granted, that likely makes for a smaller dinosaur (which isn't what the writers wanted, I guess), but going with a pack of those? The sub-plot of weaponising dinosaurs was there, so why not use it?
Second, I didn't like the "good dinosaurs vs. bad dinosaurs" thing they had going. Especially when Blue teamed up with the T-Rex to take the Indominus Rex down (coincidentally by having the Mosasaurus snatch it). Didn't like the whole idea of the tamed raptors, either. It was decently well explained, gotta admit that, but those two things really made me feel like the writers were conveying the idea that bringing animals that lived millions of years ago wasn't much of an issue - unless you're frankensteining some sort of hybrid into being, that is.