PropertiesConfiguration conf = ConfigurationUtil.loadPropertiesConfig("conf/test.properties");
JanusGraph graph = JanusGraphFactory.open(conf);

GraphTraversalSource g = graph.traversal();
JanusGraphManagement m = graph.openManagement();

VertexLabel l = m.makeVertexLabel("L").make();
PropertyKey p = m.makePropertyKey("p").dataType(Short.class).make();
PropertyKey q = m.makePropertyKey("q").dataType(UUID.class).make();
m.buildIndex("someName", Vertex.class).addKey(p).addKey(q).indexOnly(l).buildMixedIndex("search");
m.commit();

g.addV("L").property("p", (short) 1).next();
g.tx().commit();

System.out.println(g.V().hasLabel("L").has("q").count().next());
System.out.println(g.V().hasLabel("L").has("q", not(eq(UUID.randomUUID()))).count().next());

I get the output
0
1

But I would expect the output to be
0
0

since there is no vertex with label L and property q. When I remove the index the result is correct.
I assume that this is because the UUID type is handled incorrectly.
Note that this only happens if the index is on both keys (p and q).

I'm using the following configuration:

gremlin.graph=org.janusgraph.core.JanusGraphFactory
storage.backend=inmemory
index.search.backend=lucene
index.search.directory=data/searchindex
schema.default=none