The WDQS is returning results that differ from what is in Wikidata. See T112397 for previous discussions.
Example:
Run the following SPARQL query:
select * where { wd:Q21990261 p:P361 ?s . ?s ps:P361 wd:Q24772701 . ?s prov:wasDerivedFrom ?ref . ?ref ?b ?c . }
I get one row as a result:
s | ref | b | c |
wds:Q21990261-99529C15-67CB-4166-860D-C4F68336183E | wdref:d472129d472e46ce41323852d3594fefc26467fa | pr:P854 | http://www.ebi.ac.uk/interpro/protein/A1Y9I9 |
If you look on Wikidata: https://www.wikidata.org/wiki/Q21990261#P361, this is missing the stated in on the reference.
If you run the same query with replacing the wd:Q21990261 with wd:Q21135100, you'll see the query works just fine.