Because JANINO has full access to the JRE, security problems can arise if the expression, script, class body or compilation being compiled and executed contains user input.
If that user is an educated system administrator, he or she can be expected to use JANINO responsibly and in accordance with documentation and caveats you provide; however if the user is an intranet or internet user, no assumtions should be made about how clumsy, frivolous, creative, single-minded or even malicious he or she could be.
The best you can attempt is to lock the user, or, more precise, the classes generated from his or her input, in a "sandbox" to prevent the worst. This approach is similar to the concept of reducing the permissions of Java applets in a browser to, e.g., access files on the local file system.
This can be achieved as follows:
"de.unkrig.commons.lang.security.Sandbox" is available on "de.unkrig.commons".