* Why has a supermarket got a peanut-firing tommy-gun(?) under the counter?
** It's my understanding that most store clerks keep guns under the counter in case of robbery or something. Jake just shoved a can of peanuts into the firing chamber.
* If Chieftain and the Divas are better, more experienced agents, why is every stage ''harder'' if you play as them? Wouldn't it logically be the other way around, where Spin and J would have a more difficult time due to not being as skilled?
** Think of it as the more experienced agents get more difficult missions.
** Which doesn't make that much sense since they're the same exact missions the agents go on.
* If Colonel Bob did dig through the earth, why would he have ended up in New York?
** Bad aim.
** He didn't dig through the Earth - it's just stated that he dug a long tunnel. If he did dig straight through the Earth he would have been burnt to a crisp by the heat of the core anyway. Besides, that was before he had the machine that could dig through "even the toughest ground", so likely he wouldn't have been able to dig right through the Earth anyway.
* There's one bit of FridgeLogic that has been recently discussed: In the DownerEnding for "A Christmas Gift," it flashes forward 10 years into the future to a ''very'' desperate Lucy. Problem is, the Rhombulan invasion takes place shortly after you get the good ending for the level, and Lucy's hope was what started the ClapYourHandsIfYouBelieve intro. So what ''did'' happen to the Rhombulans in the bad ending?
* How do the agents follow Sam while dancing?
** For that matter, why don't the agents just take Sam home?
* Why don't the zombies attack the agents?
** Because they're too busy worrying about the guy shooting peanuts at them.
* Cap White aims to defeat Mr. Virus, who intends to rip off her clothes. This is Fridge Horror when you remember that viruses penetrate white or red blood cells for the sake of reproduction.
* At the comic scene of the last level, some people were turned to [[TakenForGranite stone]] , But even after the song , [[BigLippedAlligatorMoment they were never mentioned again]] , What happened to them? [[NightmareFuel Are they dead!?]] Who knows?
** Maybe the destruction of the Rhombulans' mothership somehow reversed the effect.
** And even if not, the Elite Beat Agents were turned into stone too, and were revived. If it was done once, it could be done again, especially given the crazy universe EBA is set in, and how effective the EBA are. At worst, the petrified people will have to wait a few days before being rescued by EBA tying up the loose ends.
* Chris's producers were yelling at him for making terrible movies. If you look at the clapboard during "Makes No Difference" when it appears, you'll see that the production company is "Nintendo Pictures". Yes, it's a CreatorInjoke, but it [[VideoGameMoviesSuck also makes some sense]].