Make sure beancount is installed and set the path on the settings page.
The linter package is required, too.
pip3 install beancount
apm install linter-beancount
Linter: Lint Linter Beancount: Run
'atom-text-editor': 'alt-b c': 'linter-beancount:run'
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.