This is not mentioned as an issue in the report, but argued to be an inconsistent by the "good ISIS" (pdf of their article on that here: http://isis-online.org/uploads/isis-reports/documents/IAEA_Iran_Report_Analysis_31May2019_Final.pdf).The report did however flag up questions about the number of advanced centrifuges Iran is allowed, which is loosely defined in the deal.
The IAEA said Iran had installed 33 advanced IR-6 centrifuges, machines that can enrich uranium, although only 10 had been tested with uranium feedstock so far. The deal allows Iran to test up to 30, but only after 8 1/2 years have passed. The limit before then is a “grey area”, diplomats say.
The "good ISIS" are disliked in the scientific community for having a political bias.
For example the ISIS report says:
To me, I don't see an inconsistency as only 10 have been tested with uranium, which is exactly what the limit they quote says Iran can do."This number of deployed [IR-6] centrifuges  is far in excess of what is a reasonable interpretation of the deployment rate implied in Iran’s long-term enrichment plan, which stipulates:
Between years 1 to 8 and a half (of the JCPOA)…[Iran will] continue the testing of the IR6 on single centrifuges and intermediate cascades (testing with uranium of roughly 10 centrifuges and then roughly 20 centrifuges, with each of these groups being tested with uranium for approximately equal time periods.
The IAEA appears unable to state that Iran remains within a reasonable interpretation of the limits of this provision, since it is above even the limit of 30 IR-6 centrifuges that it may operate starting in year 8 or 8.5"
The bigger issue is IR-8 centrifuges. Salehi recently said Iran had installed 3 of these (up from 1 - which was accepted to be permitted), but I'm not sure what the relevant limit on that is. IR-8 centrifuges have been tested for over 3 years now, and normally they take 7-10 years to be tested etc and enter mass production. The IR-8 centrifuges are 20x more efficient than the IR-1 centrifuges that Iran currently operates, meaning that in about 5 years time Iran's break-out capability will basically be ensured [Iran is not allowed to install more advanced centrifuges until 2024 under the JCPOA, so that is good timing...).