In the past I've worked on projects where the .ruby-version checked into git specifies a ruby version not recognized by rbenv. Typically this can happen when the ruby version is specified with patch version while rbenv omits it.

Consider a .ruby-version file containing 2.1.3p242. This version is listed as 2.1.3 by rbenv (while RVM and others may list it differently), and it isn't recognized due to the patch version (though the version in rbenv is actually 2.1.3p242). There's a plugin called rbenv-aliases that addresses this problem.

You can install the plugin with the following commands:

mkdir -p ~/.rbenv/plugins
git clone git://github.com/tpope/rbenv-aliases.git \
  ~/.rbenv/plugins/rbenv-aliases

Then, running the command:

rbenv alias 2.1.3p242 2.1.3

will cause rbenv to recognize 2.1.3p242 and set the ruby version to 2.1.3.

However, this plugin must be used with caution. You could say rbenv alias 2.1.3 1.8.7, which is a lie! The plugin comes with a command for removing any incorrect aliases rbenv unalias 2.1.3.