I figured it out, I'll provide the details on the off chance that anyone else runs into this problem.
Basically org.eclipse.jetty.osgi.boot.utils.internal.DefaultFileLocatorHelper checks to see if the class name is "org.eclipse.osgi.baseadaptor.bundlefile.FileBundleEntry" which it is in Kepler, but in Luna it is "org.eclipse.osgi.storage.bundlefile.FileBundleEntry" so the returned File ends up being null. It was addressed in this bug
https://bugs.eclipse.org/bugs/show_bug.cgi?id=431892 which was not fixed until Jetty 9.2.0.
I could not upgrade my app to use Jetty 9.2.0 easily (long story), so I went with a different solution which was to provide my own helper class called org.eclipse.jetty.osgi.boot.utils.FileLocatorHelperImpl which is in a fragment whose host plug-in is org.eclipse.jetty.osgi.boot. The BundleFileLocatorHelperFactory finds my helper class because it looks for an alternative class with exactly that name before using the DefaultFileLocatorHelper. For the implementation of my class, I used a slightly modified version of the updated DefaultFileLocatorHelper from Jetty 9.2.0, which already accounts for the *BundleEntry classes being moved.
Thanks and good luck!