An EMF EPackage namespace and RDF namespace mismatch can occur if one or both do not end in a / or #. EMF is tolerant of an EPackage ending without a # or /; in RDF it seems more common to have a # these days, but there are cases of /. Jena will assume a # if the RDF namespace is missing either # or / (double check this).
At the moment, the Resource is cleaning EMF Epackage namespace URIs by assuming a #. Similarly, when matching the RDF namespaces to EPackages, the # or / is removed if nothing is matched on the first attempt (it assumes the EPackage is missing # or '/').
These assumptions could be configurable options or handled more gracefully.