The isTransitive(OWLOntology) method in uk.ac.manchester.cs.owl.owlapi.OWLObjectPropertyExpressionImpl returns always true. This is also the case with other is* methods like isAsymmetric, isIrreflexive, isReflexive, ... . The reason could be that these methods check for nullity instead of emptiness.
See 3017636
Sorry, wrong duplicate. The correct one was reported by Thomas Scheneider. 3005709