This happens to me all the time.
At one point in the sequel, Aquila (one of the new characters) just outright turned herself into the 11th Doctor Who...apparently, she needs to be played by Matt Smith. She also puts her coat (ankle-length, double-breasted military) on doorknobs regardless of if there is a hanger nearby, and she is a coffee fiend.
None of this was planned when I started writing the story.
There's also a pretty big character spoiler coming in a couple of chapters of Re:Apotheosis for Captain Infinite, which was also not present in the original outline.