At the end of 5, Regal undergoes a Heel–Face Turn and gives a talk to the heroes like a calm father figure. What makes this scene amusing is that said speech is accompanied by his evil angry mugshot from his villainous days. This was fixed in the Double Team DS re-release, where he gets a new mugshot that reflects his reformed status more.
In 6, a plumber's Navi loses his tool program, and Lan and Mega Man find it stuck to a Mettaur's head. Lan tells Mega Man to delete the virus, but Mega Man doesn't want to since the program looks harmless and doesn't want to touch it.
Every time the security bots ask to see Lan's ID in the sixth game.