In "Pups Save the Bunnies", after Ryder lets Skye keep one of the bunnies that had stowed away on Skye's helicopter, two more appear. It is unknown if Ryder let Skye keep the other two and no one seems to know where these two bunnies came from. It possibly meant as a play on the bunnies ability to multiply (as they are well known to reproduce quickly).
In "Pups and the Pirate Treasure", the Eagle is shown to prey on wild bunnies for food. In the real world, due to their large populations certain species of bunnies (such as the Eastern cottontail of Eastern North America) often form a major component of several predators' diets.