That's probably because the version of Atom or langauge-agda you are using is too old. Humans were (and still are) highlighting source codes with regular expressions until very very recently. Please consider upgrading them to the latest version. If you are getting some scary error during the upgrade, please uninstall and then reinstall language-agda
apm develop language-agdaatom -d ~/github/language-agda
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.