please try latest on 9.1 (9.1.13 ATM) ... this is an auto-loading issue that might go away.
if it persist than try to eager load your application -> as (lazy) loading in multiple threads, without a GIL, will always have some (more or less visible) race conditions ...

@kares The application is already configured to use eager load and it should be able to work with the threaded web server in my case passenger server.

config/environments/production.rb

  # Eager load code on boot. This eager loads most of Rails and
  # your application in memory, allowing both threaded web servers
  # and those relying on copy on write to perform better.
  # Rake tasks automatically ignore this option for performance.
  config.eager_load = true

Am I missing anything here, except upgrading jRuby to the latest version?

nope, except maybe activerecord-jdbc-adapter not supporting Rails 5.x ... depends on particular adapter on how well it works. anyways just give upgrade a try and if the issue persist try to come up with a minimal reproducer piece.

since there's finally some AR-JDBC 50.x releases, this should be re-evaluated using those (and latest 9.1)

... no further feedback here and since desc is very vague - closing. we ideally need a reproducer.
anyway before doing that you should re-run with latest 9.1/9.2 as well as updated activerecord-jdbc-adapter.