Killed only one character - Toriel, right at the start
before I figured how the game works. It still haunts me.
The Toriel fight is the only part of the game I really dislike. The "correct answer" isn't something you get by playing/learning the game's systems/understanding the feedback, but by ignoring that feedback ten or twenty times in a row; this is game design possible only in an age where people have gotten confused between playing-games and reading-about-games-on-the-internet. (And I know I'm not the only one who feels this way; I remember reading a review that argued the fight basically undermined the point of the game.)
But in my case it's more due to a personal pet peeve of mine: when games intend (and even advertise) a nonviolent course of action but then hide it away in an undocumented trick, upgrade, or NewGame+ mode, or something that can't reasonably be done by a new player on their first playthrough.