Owlready2
registers all properties when loading them. For the map key, it only uses the name of the property. However, names are not unique, but only in combination with the namespace/ontology name.
This leads to problems when creating an ontology. I specifically import two ontolgies that both provide a property with the same name. When saving the ontology, Owlready2 uses the wrong namespace to prepend to the property name, making the generated ontology inconsistent.
I would have created an issue for this on BitBucket, but this does not seem to be possible.