BaseDataFileFactory has a public constructor and a public boot() method. Arbitrary code running in the JVM may be able to instantiate a BaseDataFileFactory outside of Derby's authentication mechanisms and so acquire the ability to read/update Derby-managed data with the privileges granted to Derby. Arbitrary code may be able to interfere with the normal operation of Derby and may be able to corrupt data.
This is just an observation based on casual code inspection. It may be that there are mechanisms in place which frustrate these attacks. I have not tried to exploit these potential vulnerabilities myself.