To fix the issues caused by just one rule, you need to combine
--fix --rule with
--no-eslintrc. Otherwise your rule will just be merged with your existing configuration and all fixable issues will be corrected. E.g.
$ eslint --no-eslintrc --fix --rule 'indent: [2, 2]'
Depending on your setup you’ll need to re-add mandatory settings from your ESLint configuration to the command line for the lint run to succeed. In my case I had to use
$ eslint --no-eslintrc --parser babel-eslint --fix --rule 'indent: [2, 2]'