Just seen this error for the first time. Have we recently changed the version that we're running of Blazegraph ?

The following query is failing apparently instantly, throwing a "java.lang.IndexOutOfBoundsException: Index: 2, Size: 2" (Try it!)

PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX schema: <http://schema.org/>

    SELECT (COUNT(DISTINCT(?item)) AS ?count) WHERE {
       ?item wdt:P31/wdt:P279* wd:Q56061.
       MINUS {?item wdt:P373 ?commonscat} .
    }

Added:

The issue appears to be specifically triggered by the path search statement.

Putting in ?item wdt:P31 wd:Q5 instead of ?item wdt:P31/wdt:P279* wd:Q56061 in the above the query runs fine ... or does until it times out, at least.

So the problem appears to be an interaction between MINUS and the path search.

Other variants of negation -- eg FILTER NOT EXISTS { ... } or OPTIONAL { ... } FILTER (!bound(...)) -- don't seem to have the problem; so it does seem probably a bug in the implementation of MINUS.