I encountered a problem with my rails project that uses yanked / deprecated gem (example: coffee-script-source-1.1.3) but I cannot just update this gem, because my other gems has a dependencies with this. The solution is:
If you can still download the gem file from RubyGems.org download it, then paste the downloaded gem to your rails' project
/vendor/cache - Create cache directory if needed.
then run bundle install