According to the OWL 2 specification, the "the graph G MUST be empty" after parsing an RDF graph into OWL objects. If this is not the case, the OWL object model is not defined for the input, and the input must be rejected. The OWL API seems to ignore this requirement at least in some cases.
The issue is illustrated by the OWL 2 test case http://owl.semanticweb.org/page/TestCase:WebOnt-I5.26-010 which has triples in its conclusion that do not belong to any axiom. The OWL API wrongly accepts this input and classifies it as belonging to all profiles (which cannot be right, since profiles are only specified in terms of functional-style syntax which the example ontology does not have at all).
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