If you have the atom-beautify package installed, you can enable/disable auto-format on save for each supported language separately:
atom-beautify → scroll waaay down to
Language Config - LangXYZ - Beautify On Save (with LangXYZ being the language configured).
If you don't have extra packages installed, it might the whitespace package, which comes with Atom and is enabled by default:
You can either click
Disable and be done with it (I did :-)), or you can disable the package selectively via entries in your
config.cson file, as documented on the package page itself.