The new option Auto Indent On Paste is unusable with languages like CoffeeScript (or Python, Haml, etc.).
This is related to https://discuss.atom.io/t/coffeescript-auto-indent-broken/ .
However, this is a global option, so it cannot be disabled for CoffeeScript files (or can it?).
I guess the best behaviour when pasting CoffeeScript lines should be: just paste the lines and don’t bother trying to fix indentation.