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- In Episode 53 of Rockman.EXE, while having a party at Yaito's house (whose participants are Netto and co., Masa, Miyuki, Saloma, Mariko, and even the ex-World Three executives), Masa tries to cheer up Mariko by giving him a sea bream. Without looking at her, when he receives a response, he turns around and finds that Madoi was the one who accepted it, biting on and holding onto it like a cat.
- Episode 14 has Yai hijack Lan, Mayl, Rush, and Ms. Mari using a robot elevator and flies them around the world. The dub adds some lines.
Lan: We're over the ocean!Mayl and Ms. Mari: Close the door, close the door!Lan: *sees wild lions outside* Rush, you're a dog, take care of those cats!Rush: Nuh-uh!Lan: It's cold! *face freezes* Really cold!Ms. Mari: Oh look, penguins! How cute!Lan and Mayl: Ms. Mari!Mayl: Its an undersea adventure.Ms. Mari: What's keeping the water out? *elevator fills with water* Oh dear! Why'd I say that?!Lan: I know!
- Once Yai's video game data is retrieved, the others aren't too happy to find out the bad guys were based on them.
- GutsMan growing like an ape and taking Roll hostage like in a King Kong movie.
- Episode 22 is full of funny moments, the highlight being the ending, in which BubbleMan gifts his secret bottle cap figure to his boss and leader of the Darkloids, ShadeMan. The latter's reaction is priceless.
- Mist Man's hilarious Heel–Face Revolving Door where he switches between attacking Cross Fusion Mega Man and Sword Man and Fridge Man since Mayl and Ms. Yuri are playing keep away with Mist Man's lamp and he has to obey whoever's holding it.
- In episode 33, Video Man creates an army of Mega Man copies to fight Tomahawk Man, but he made too many copies making them small and allowing Mega Man to defeat them all with just one swing of his axe.
- In episode 36, an evil version of Megaman manages to take his place and wreak havoc. How does Lan see through the deception? At the start of the episode, he used a joke chip on Megaman that covered him in bandages, and when Megaman takes them off Lan didn't tell him that he missed one on his butt. When Lan noticed that Evil!Megaman didn't have one, he realized he was dealing with an impostor.
- When Lan's friends see Chaud's haircut in the manga, they compare it to a chick coming out of an egg.
- Megaman Hub Mode initially serves as an unstoppable Super-Powered Evil Side that puts Lan in critical condition and makes Megaman go berserk. When they first manage to break him out of it, Protoman immediately punches Megaman in the face. Chaud also does this to Lan in the real world.
- Chaud in general is much funnier in the manga. In the anime, he was just a cool guy stoic, but in the manga, he's much more likely to loose his cool and give us a few laughs.
- Lan and co try to train Megaman in order to control his rage by insulting him and then seeing if he can ignore them. HINT: Evil!Megaman becomes stronger if Megaman becomes angry in his presence. Megaman eventually goes berserk and starts to attack them in a hissyfit.
- After Lan and Megaman first unlock Hub Style, they don't know how to activate it again in order to show his friends, so they come up with a silly-looking imitation. Then, when they fight Protoman, they attempt to activate Hub Style, and accidentally activate the fake. Protoman promptly punches Megaman in the face.