The revelation about Small One and the conditions of her life leading up to her death and Elise being stuck with her skeleton for a long time are as much Nightmare Fuel as are they Tear Jerkers.
Bridges' hallucinations can be pretty unsettling, especially when they start telling him to kill himself, kill others, or both. Usually with fire.
Isla Sorna has Troodons of its own. They are still just as terrifying as they were in Jurassic Park: The Game.