I decided to attach a remote debugger to see where these were coming from and appears that they are generated from:
In that method we loop through a metadata repo, finding all the IUs and grab the FileName property on that IU. In the case of translation fragments, I don't appear to have a filename, so an error is logged.
Some information about the repository: location: file:/home/irbull/eclipse/eclipse/configuration/org.eclipse.osgi/bundles/834/data/1969065986/ name: extension location metadata repository: file:/home/irbull/eclipse/eclipse/.eclipseextension
I don't know anything about the FileName property, so I'm pretty much stuck on where to go next. If anyone has any ideas, please let me know and I will continue to try and debug this issue.