I looked for true duplicates at Wikidata using the query
SELECT DISTINCT ?item1 ?item2 ?sitelink WHERE {
?sitelink schema:about ?item1, ?item2.
?sitelink schema:isPartOf <https://sv.wikipedia.org/>.
filter(?item1 != ?item2)
}where I changed 'sv' for different languages. I've found a few cases where the values of sitelinks were different in Wikidata GUI and SPARQL endpoint.
The SPARQL query says that Q19929406 contains https://sv.wikipedia.org/wiki/Ljudniv%C3%A5. But this is not the case at Q19929406. Also Q6766777 has https://en.wikipedia.org/wiki/Mark_Bonner in Blazegraph, but not in Wikidata GUI.
Probably there are other cases like that. It seems the wdqs-updater for some reason has not caught those changes.