I'm following the advice to report this, found at https://wikitech.wikimedia.org/wiki/Wikidata_Query_Service#Known_limitations
I ran a bot on Wikidata to change some qualifiers on taxon names from 'instance of' to 'has role'. The bot used this SPARQL query as a pywikibot generator to identify the items that required the change.
The query still returns the following rows, even though the bot changed the qualifiers days ago.
*Q309241
*Q2711806
*Q3076721
*Q5023514
*Q305102
*Q311383
*Q2105518
*Q2130100
*Q2397476
*Q21191097
*Q675783
*Q2117271
*Q2863460
*Q3130156
*Q27074621
*Q20904489
*Q25096206
*Q28042286
*Q28046026
*Q14828500
*Q605846
*Q618283
*Q7104363
*Q19595888
*Q19607707
*Q19838081
*Q5705943