Updater logs show these messages:
05:26:33.222 [update 5] INFO o.wikidata.query.rdf.tool.rdf.Munger - Unrecognized subjects: [http://www.wikidata.org/entity/statement/Q63199357-bb5c53bf-4c82-1b40-a7bc-21396dc9332b] while processing http://www.wikidata.org/entity/Q63199357. Expected only sitelinks and subjects starting with http://www.wikidata.org/wiki/Special:EntityData/ and http://www.wikidata.org/entity/
This should never happen while fetching Wikidata updates, so we need to investigate what's going on there, might be some bug in Munger.