/usr/lib/ruby/site_ruby/1.9.1/phusion_passenger/utils.rb line 325 requires bundle.
Line number is from passenger-3.0.17, but this is a trivial fix.
In this case bundler is a dependency of the application you are trying to run, as indicated by the Gemfile presence. The passenger rubygem doesn't express a dependency on bundler either. If you still feel that this wrong, then please discuss this with upstream.