It looks like inconsistent Pellet behaivour:
This fragment causes Pellet generate warning, and report inconsistency in the SWOOP:
  <rdf:Description rdf:about="http://www.owl-ontologies.com/animals.owl#isStriped">
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
    <rdfs:domain rdf:resource="http://www.owl-ontologies.com/animals.owl#Tiger"/>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.owl-ontologies.com/animals.owl#Tiger_1">
    <rdf:type rdf:resource="http://www.owl-ontologies.com/animals.owl#Tiger"/>
    <animals:hasColor
rdf:resource="http://www.owl-ontologies.com/animals.owl#Yellow"/>
    <animals:isStriped>true</animals:isStriped>
  </rdf:Description>

and the following does not
<?xml version="1.0"?>
<rdf:RDF
    xmlns="http://www.owl-ontologies.com/Ontology1147788277.owl#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
  xml:base="http://www.owl-ontologies.com/Ontology1147788277.owl">
  <owl:Ontology rdf:about=""/>
  <owl:Class rdf:ID="Class_2">
    <rdfs:subClassOf>
      <owl:Class rdf:ID="Class_1"/>
    </rdfs:subClassOf>
  </owl:Class>
  <owl:ObjectProperty rdf:ID="objectProperty_1">
    <rdfs:domain rdf:resource="#Class_1"/>
    <rdfs:range rdf:resource="#Class_2"/>
  </owl:ObjectProperty>
  <owl:DatatypeProperty rdf:ID="datatypeProperty_3">
    <rdfs:domain rdf:resource="#Class_2"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
  </owl:DatatypeProperty>
  <Class_2 rdf:ID="Class_2_2">
    <objectProperty_1>
      <Class_2 rdf:ID="Class_2_3">
        <objectProperty_1 rdf:resource="#Class_2_3"/>
        <datatypeProperty_3 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
        >false</datatypeProperty_3>
      </Class_2>
    </objectProperty_1>
    <datatypeProperty_3 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
    >false</datatypeProperty_3>
  </Class_2>
  <Class_2 rdf:ID="Class_2_4">
    <objectProperty_1 rdf:resource="#Class_2_2"/>
    <datatypeProperty_3 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
    >true</datatypeProperty_3>
  </Class_2>
</rdf:RDF>


Here is stack of Pellet:
org.mindswap.pellet.exceptions.InconsistentOntologyException: Cannot do
reasoning with inconsistent ontologies!
	at org.mindswap.pellet.KnowledgeBase.ensureConsistency(KnowledgeBase.java:778)
	at org.mindswap.pellet.KnowledgeBase.retrieve(KnowledgeBase.java:2307)
	at org.mindswap.pellet.KnowledgeBase.getInstances(KnowledgeBase.java:1653)
	at
org.mindswap.pellet.jena.PelletInfGraph.instanceIterator(PelletInfGraph.java:896)
	at org.mindswap.pellet.jena.PelletInfGraph.findInABox(PelletInfGraph.java:394)
	at
org.mindswap.pellet.jena.PelletInfGraph.findWithContinuation(PelletInfGraph.java:192)
	at com.hp.hpl.jena.reasoner.BaseInfGraph.graphBaseFind(BaseInfGraph.java:333)
	at com.hp.hpl.jena.graph.impl.GraphBase.find(GraphBase.java:241)
	at com.hp.hpl.jena.rdf.model.impl.ModelCom.listStatements(ModelCom.java:364)
	at com.hp.hpl.jena.rdf.model.impl.ModelCom.listStatements(ModelCom.java:369)
	at com.hp.hpl.jena.ontology.impl.OntClassImpl.listInstances(OntClassImpl.java:637)