Execjs, libreadline, libsqlite3, lib-postgres, (older)nokogiri etc. Quite a lot of the headers keep being a problem. Not major, often a mere ddg+apt-get away, but still annoying. It does get problematic when you have multiple apps depend on different libreadlines, for example.
And I'm not often deploying java, but at least the runtime and tooling has become omnipresent. The latest deploys were a mere "move all files there, and restart the service". With Rails you at least need to rebuild the gems.
Often java-services are an `apt get jenkins` away. There is no equivalent apt-get gitlab or apt-get mastodon that just sets up the stack entirely. But that is probably due to their popularity more than technology.