After buying and/or collecting the three gift items from island shops and giving them to Roll, she will be missing from the cockpit, leaving Data alone. If you go to the bathroom after talking to data, a black screen appear with Roll yelling at you, implying you walked in on her taking a bath. Mega Man will do his victory pose right after this. If you go into Roll's room after this and read her diary she will mention this and another time that Mega Man walked in on her, referencing the Easter egg from the first game. Strangely, this scene is also the trigger for Roll to give you 10% discount on Weapon upgrade prices.
In the Mayor's house on Manda Island, you can take a test to get some items. One of the random questions is about the oldest heavyweight Boxer. One of the incorrect answers is Balrog, the boxing character from Street Fighter.
During the end credits, Susan Roman is credited as "Rock" instead of Mega Man.