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)

Ron Alford wrote:

>Ron Alford <ronwalf@umd.edu> added the comment:
>
>Here's the inconsistency:
>WARNING: Inconsistent ontology. Reason: Plain literal "3:15:00 PM" does not
>belong to datatype http://www.w3.org/2001/XMLSchema#time. Literal value may be
>missing the rdf:datatype attribute.Timer Pellet Processing Avg: 1430.0 Count: 1
>Total: 1430
>
>Hopefully we can get that warning back to SWOOP
>
>----------
>status: unread -> chatting
>
>___________________________________________________
>Mindswap issue tracker <issue_tracker@mindswap.org>
><http://www.mindswap.org/issues/issue292>
>___________________________________________________
>
>
>  
>

Wow!  That was simple.  If that message were forwarded, it would be very 
easy to respond to.

Here I was, going through a bunch of DL debugging trying to find the 
inconsistency.

Thanks!

Dean

Here's the inconsistency:
WARNING: Inconsistent ontology. Reason: Plain literal "3:15:00 PM" does not
belong to datatype http://www.w3.org/2001/XMLSchema#time. Literal value may be
missing the rdf:datatype attribute.Timer Pellet Processing Avg: 1430.0 Count: 1
Total: 1430

Hopefully we can get that warning back to SWOOP

The enclosed ontology isn't where the problem is, but the one it imports is
online, and will show the problem when you load this one into SWOOP.

There are some complicated uses of subproperty/transitive property going on,
that results in a bug somewhere in this ontology.  

When you turn Pellet on in SWOOP, it of course detects the inconsistency, but
the error message says, 

Inconsistent ontology Reason: No inconsistency was found! There is no
explanation generated. 


Someone is getting his signals crossed here. 

I am pretty sure that the ontology really is inconsistent, but it would be nice
for SWOOP and Pellet to agree about it.