Writing Java programs was a blessing to developers who did not have to bother about the platforms on which the programs would run. But as Java became enterprise quality and an enterprise darling, developers have to be aware of JVM issues and other platform issues. They should also befriend their sysadmin and their DBA, as they are as relevant to your project success as your quality code is.
Googling, I found this link, which talks of why Java is a nightmare for Sysadmins. Java Sucks For Sysadmins
Java IO abstraction creates the most problems on various platforms in my opinion.
Get to know swap spaces, file descriptors, ulimit command. Just because you know java.io.File, you are not an enterprise developer. Kidding!