There are more than a few. First, there is the issue of how Chomper got off that island, if and his parents did too. Presumably, because Ruby says that she told his parents that she'd take care of him, they got off the island too, or Ruby's family visited the island at one point.
Then, there is the matter of how Red Claw came to be such a menace. No explanations are given. And why Chomper's parents aren't with him.
There are many others, I am sure.