Plot hole: Ben demonstrates for the FBI that he has not only invented gear that allows animals to speak English, but trained ordinary rodents to a level on par with Navy Seals. The FBI laughs at him and cuts his funding, a plot hammer so G-Force can escape and save the day. Are they kidding!?! Even if the info G-force brought back is wrong, Ben has created agents that can repeatedly infiltrate almost literally any place on Earth. No government agency would pass up such a huge intelligence gathering tool.
Continuity mistake: Watch carefully during the scene where Hurley gets launched by the sprinkler. When Darwin says, "Come on, soggy," as he is walking away, the camera pans back to show Hurley still lying on the concrete, we see little guinea pig footprints in water on the sidewalk. They weren't made by Hurley because he hadn't moved and Darwin had dodged the water and was completely dry. Nor did he walk in the water either.
Continuity mistake: After getting the 3 sphere car and FBI guys starts to hunt them. In the first jump after Juraze says " here comes the bad guys". When they land from the jump the FBI car front left wheel gets flatten and the front lower left bumper light gets loose. Scenes after its fixed again. (00:55:00)
Other mistake: If you watch very closely at the end, when Hurley is found beneath the rubble, Blaster lets go of the heavy steel box that was on top of Hurley before Darwin actually pulls Hurley free, so Hurley should have really been dead.
Factual error: Another problem with Speckles the star-nose mole. Star-nose moles live in "wet lowland areas" (Wikipedia) but in the film, Speckle's history is shown and his home used to be a field with undulated small hills.
Factual error: When Mooch is leaving the pet shop he goes through a bunch of Venus fly traps and they instantly snap at him. Venus fly traps don't close their leaves instantly, they wait for the prey to land and move around, closing tighter the more the prey wiggles.