I found myself in a pretty confusing situation today when I was trying out Rails 3.1.rc1. In my Gemfile, I specified Compass to be installed from the github repo and bundler did just that. But I had to run Compass's executable in my rails app and I had no clue as to how to do it, because my rvm gemset for trying the RC version of Rails doesn't have Compass installed in the gem environment. So running the following command, generated a command not found error.
Bundler installs it local to the application, when you choose to install from the git repo, so the executables aren't in your gem path. In such situations, bundle-exec comes handy.
Will run the compass command with it's arguments in the scope of the bundle (I'm referring to the gem dependency environment managed by bundler not to git-bundle).