Other mistake: When Drek lands in New Quartu, his crashed shuttle is facing towards the Deplanitizer's direction. His shuttle should be facing the other way since he was launched straight to New Quartu.
Plot hole: When Drek lands in New Quartu, birds are heard chirping. It is unknown how they survived each planet's destruction.
Continuity mistake: In the first scene, the old alien man comes to pick up his spaceship and Ratchet instructs him to "Now, let's fire up that mag booster." The old alien pushes the switch forward to start the mag booster. Later in the movie, Ratchet flips the switch backwards to "engage mag booster" as Clank commands. (00:06:30 - 00:26:30)