Looks like your app's ./bin/rails is a stub that was generated by Bundler.

In Rails 4, your app's bin/ directory contains executables that are versioned
like any other source code, rather than stubs that are generated on demand.

Here's how to upgrade:

  bundle config --delete bin    # Turn off Bundler's stub generator
  rake rails:update:bin         # Use the new Rails 4 executables
  git add bin                   # Add bin/ to source control
:
:
:

とか言われる。
なぜだ？と思ったら、

# conig/deploy.rb
set :linked_dirs, fetch(:linked_dirs, []).push('log', 'tmp/pids', 'tmp/cache', 'tmp/sockets')

にbinが入っちゃってた。
デフォルトのコメントの内容を書き換えて設定した時に、消してなかったっぽい…。

参考