TL;DR:
Don\'t run bundle within an existing git repository. Weird things will happen without any error messages.
Original Question:
One of the things bundler did for you is start a local git repo to version-manage your gem code. Check that you have added the file in git
git add lib/gem_name/missing_file.rb
Bundler generated gems use git internally to track "membership" of source files for the gem. You can see this in the .gemspec where it uses backticks to call out to git and generate a file list:
gem.files = `git ls-files`.split($/)
Note this also means you should pay attention to what you list in .gitignore