In the original version of Episode 7, Chapter 3, Centaur Man was introduced as a new character who was the Robot Tournament fighting champion, and it was made clear that he was not created by Dr. Wily. However, Centaur Man had already been introduced at an earlier point in the series as one of Dr. Wily's new Robot Masters, and this fact had slipped the author's mind. The error has long since been corrected, and the author had to write a slight retcon to Centaur Man's introduction as a result of this. To this day, when the author sneaks any in-story references to the Robot Championship Tournament as being a complete disaster, he is usually making a reference to this error.
In Episode 10, Chapter 9, the author forgot to delete a production note that he left to himself in regards to a small paragraph within a scene. Both the note and the paragraph were removed later that night.
Episode 11, chapter 10, was originally posted with a working title rather than the finalized one. It was corrected almost immediately.
QN-60 and Castor originally had death scenes written out, but the author changed his mind.
Doc was considered to survive, but it was decided his death would have more impact. His death was also originally scheduled for Friday the 13th, but the author felt it would be obvious that something bad would happen then.
Originally Tron Bonne would've had an obsessive crush on Dr. Wily, but this was changed due to being too much of a stretch. (Her age wasn't finalized at that point in time.)
In Episode 8, originally Roll was going to be trapped in the tower with a young male officer, and the two would have developed a friendship during the situation. This was cut because too much was going on and it would enhance the suspense with her being alone.
In Episode 9, originally ProtoMan wasn't going to take charge of Wily's operations. He and Wily would have been very cold to each other, and his demotion at the end would have come purely from objecting to usage of the Black Hole Bomb. There still would have been a clash between Proto and Wily, but it wouldn't be as heavy.
The author said that if the female RM was with the Killers she would have been the calming voice among them, and they probably would have won their fight against Mega Man.
A battle against Top Man in Episode 8 would've had Cut Man breaking the fourth wall, but it was decided it was too goofy.
One draft of an Episode 9 chapter had Metal Man living, but it was decided a death suited the scene better.
Originally the Mega Man Killers, who debuted around Episode 10, were slated to appear in Episode 4, where they'd be destroyed. The author decided that introducing them and killing them off so quickly wouldn't do, and that they could possibly carry their own episode, so he used different Robot Masters to be destroyed.
Kalinka's cutting scar was going to be revealed in Episode 6, with ProtoMan noticing it, but it was moved to Episode 10 with Mega Man noticing it as the author felt it'd fit better there.
In the climax of Episode 10, originally, Ballade was going to blow himself up because he was shamed after being labeled a failure and never had the respect of his comrades. But after having him debate morality with Mega, and the refusal to kill those who were not enemies, the author decided that his sacrifice to try and stop Wily from detonating the bombs was better.
Mr. Black's wife's name was originally named Sonya instead of Tonya.
One plot element of Episode 13 that was scrapped would be that Kalinka was going to see Splash Woman controlling Mega Man to kiss her, and Splash would have kissed him to hurt her. Kalinka would have to later be convinced that Mega wasn't acting that way of his own free will. It was scrapped because it would cast doubt on their relationship from that point on, and the entire episode had to be rewritten to account for the change.
Originally Luna was going to be a female Stardroid, and possibly one who had a romantic connection to Terra. But that was scrapped when the author decided to just make Luna be the Evil Energy Robot from MM8, who he wanted to include anyway.
Originally the Conduit was Mitchell Deacon, the idea being that if he targeted himself, he'd be dismissed as a suspect. It was changed due to not wanting to tarnish the Ruby-Spears cartoon, which introduced Deacon as a supporting character on the side of good. The real culprit, Rehnquist, also wasn't going to be related to the Loaths originally, nor would he be in contact with Glyde, but it was changed to add more game characters.
Episode 3's title was originally "Doc," but that was spoilery. The author also considered "The Worst Week" and "The Darkest Week," but didn't like them.
"Mega Sis" was the working title of Episode 8 because Roll was heavily featured. Even the files were titled "Mega Sis".
The working title for Chapter 108 was "The Next Conversation," meant to be a reference to the chapter "The Conversation" from Episode 5. But this conversation wasn't really the next one because Mega and Proto had already had two meaningful conversations since then.
The working title for Project G-2 was "Dr. Wily's War Machine."
The working title for the Episode 10 epilogue was "Hitting Rock Bottom." This title was later used in an Episode 11 chapter.
Episode 11, chapter 10 was originally called "Darkest Before Dawn." The author decided to save that title for Episode 11, chapter 12.
Episode 13, chapter 2 was originally called "I Put A Spell On You."