That's really not a bug.
Modules view reference the Available libraries.
When you will export your job, only the really required libraries will be added to your job. Else it would be pretty a quite big export....
The really needed libraries are computed using :
* list of component of your job
* libraries referenced the specific tLibraryLoad component
If you're using some custom code in a routine, you must reference the library that must be used within the routines properties.
If you're using some tJavaXXX components, you should use the tLibraryLoad component.