When deploying with Passenger, errors such as below are shown.

# Error: The application encountered the following error: 
# You have already activated stringio 3.1.1, but your Gemfile requires stringio 3.1.0. 
# Since stringio is a default gem, you can either remove your dependency on it 
# or try updating to a newer version of bundler that supports stringio as a default gem. (Gem::LoadError)

The reason is that Passenger loads default gems which might be a different version that you specify in your Gemfile.

To change this behavior, the Passenger provides a config to disable it.

passenger_preload_bundler = off;

Once it is added, restart your application and the correct version of the stringio should be loaded.

Reference: https://www.phusionpassenger.com/docs/references/config_reference/nginx/#passenger_preload_bundler