In "Bonehead vs. Cobra", when Bone said, "And it ate everything that is not what it seems!", it is a reference to the Wizards of Waverly Place theme, "Everything Is Not What It Seems" (sung by Selena Gomez).
In Cleetus & Pals, Roccos the blue protoceratops and Bone the yellow triceratops are references to B.J. (the yellow protoceratops) and Baby Bop (the green triceratops), respectively. V. Nuss Flytrap the green hadrosaur is a reference to Riff the Orange Hadrosaur. Bit the violet brontosaurus is a reference to Brontonio (the red brontosaurus). It is unknown who Dinnosaur (the orange stegosaurus) seems to be a reference to in Barney & Friends. It is also unknown what dinosaur Cleetus's friend is.