@ScarletKittie: Yeah I was thinking about this earlier. I think it would be best to only include characters with spoken lines in the character section and then add a section called "Background Characters" in the episode pages and list all the characters who made an appearance, even if it was the mane cast. I think that's the best way to handle it.
Set it up like this (making all this stuff up for the example):
- Derpy was briefly shown behind Rainbow Dash juggling in this episode.
- Doctor Whooves was seen buying carrots in this episode.
- Twilight Sparkle, Scootaloo, Smarty Pants and Snips were briefly shown in the background in this episode.