I spent a week trying to solve a similar problem. Turned out to be the bundler gem. The system bundler on my server was a different version than the bundler version on my development machine. Check your Gemfile.lock file. If last line says BUNDLED WITH a different version as "bundle -v" from the command-line, you should work to get them on the same version.

BTW, I found the answer in this long ticket: https://github.com/phusion/passenger-docker/issues/409