* Why is an obscene amount of Mushroom Kingdom coins worth so few Beanbean coins? In the usual Mario games that take place in the Mushroom Kingdom, coins are very abundant and it would be very easy to rack up several thousands with all the bricks and underground store holds of them everywhere. Not so much in the Beanbean Kingdom.
* Maybe it's not just that the Mushroom Coins lose their value over the course of the game, but the Beanbean Coins ''increased in value'' at the same time. When Tolstar first checks the exchange rate, the prince is missing and Beanbean's capital city is under attack or in ruins already. When Peasly's bet is concluded, it's long since been rebuilt, and the kingdom is in good shape.
* In the trailer for the remake, various laugh tracks and synonyms for laughter were used in the beginning, referencing the Beanbean kingdom's secondary theme of humor and pleasure in the original game.
* The fact that the Chuckola Reserve itself attacks you (it's the Chuckolator). If you read the statue plaques back at the entrance to the woods, the last one notes that the quality of the brew may vary depending on the quality of the jokes told. When you arrive to find Bubbles telling joke after joke to the reserve, you might note that they're all pretty bad/lame jokes. No wonder the Reserve turned bad/evil if the jokes are bad.

* Shortly after you enter Woohoo Hooniversity to face off against Cackletta and obtain the Beanstar, a bunch of professors run by... except for one, who falls down, tells you that the professors from the Hooniversity are being transformed into monsters, and transforms into a Laser Snifit. After Mario and Luigi defeat him, he doesn't change back. Neither do any of the other monsters in the Hooniversity. They all simply disappear, implying that they die like the normal enemies. Now think about it. If all of the monsters in the Hooniversity were once professors, then that means [[MercyKill you were basically forced to]] [[KillEmAll kill all of them]] [[AndIMustScream so they wouldn't suffer]] [[FateWorseThanDeath a fate worse than death.]]
* When Mario gets sick via eating an Invincishroom in Little Fungitown, the Toad doctor points out the cause as Bean Fever (It's a disease that affects people not accustomed to the food in Beanbean Kingdom) and that if Luigi doesn't get the cure, Mario will turn into a bean. Said cure is Crabbie Grass that seems to be hard to come by. Then you realize that there are a [[FateWorseThanDeath near unlimited amount of beans in the kingdom.]]
* You destroy Cackletta's '''soul'''!
** What about the fact that the battlefield where you fight her in the climax, Bowletta's stomach, is on ''fire''? That has to be painful.
* The scientists that were researching the Oho-Jees learn that lighting them on fire or electrocuting them turns them into monsters and the person responsible into an Oho-Jee himself. The scientists then consider researching this phenomenon. First, [[TheSociopath they do not seem to care about the loss of a co-worker]], [[ForScience only about research.]] Second, [[ApocalypticLog the tape you find detailing this discovery is the last you hear from them.]] Remember what was said about the Oho-Jees.
* The aformentioned FridgeBrilliance regarding the Mushroom Kingdom–Beanbean Kingdom exchange rate becomes this when you realize that actually happened in real life to Zimbabwe. The bank actually printed out hundred-trillion-dollar bills, and you still could barely buy anything with them.