These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Logic: In the Recap cinematic, Captain Qwark stated his reason for not being present in Quest For Booty, and that was for shooting for a new holo-film. However, Captain Slag and Rusty Pete both had parts in the film as well, and they both had significant roles in QFB. How could they manage the time to film alongside Qwark as well?
Solution: Qwark was also filming Unicop in-between the two games. It might have been filmed first, while My Blaster Runs Hot was filmed afterwards. This would make sense, considering the amount of time and costs it would take to finish Unicop because Qwark plays a unicorn in the film, while he's just playing himself in My Blaster Runs Hot, so there's a good reason who the latter was released, first.
Harsher in Hindsight: After you've seen Azimuth go nuts and kill Ratchet in his quest to rewind time, his unceasing ranting throughout the game suddenly sounds much more unhinged than it did on your first playthrough.
Moral Event Horizon: Alister Azimuth kills Ratchet at the end of the game. Shortly afterward, he becomes the final boss and nearly destroys the entire universe. However, since Ratchet's death is undone by Clank and Alister finally sees the error of his ways, sacrificing himself to prevent the destruction of the universe he almost brought upon it, fans generally don't consider him too far-gone to be denied posthumous redemption.