Thanks for the detail. I tried to repro this issue, but it did not load these index organized tables at all. Could you try to run below queries manually to see if it contains the SYS_IOT_OVER_* tables?
SELECT Usrs.user_id
, Objs.object_name
, Objs.object_type
, Objs.created
, Objs.last_ddl_time
, Objs.temporary
, Objs.status AS status
, decode(cluster_name,null,0,1) as is_clustered
, NULL as is_in_memory
, NULL as table_type_name
, NULL as table_type_owner
, CASE WHEN Mv.CONTAINER_NAME IS NOT NULL THEN 1 ELSE 0 END AS is_mat_view_table
FROM sys.dba_objects Objs
, sys.dba_mviews Mv
, sys.dba_users Usrs
, sys.dba_tables Tbls
WHERE Objs.object_type = 'TABLE'
AND Objs.subobject_name IS NULL
AND Objs.owner = Usrs.username
AND Objs.owner = Tbls.owner
AND Objs.object_name = Tbls.table_name
AND Tbls.nested <> 'YES'
AND TRIM(Tbls.instances) <> '0'
AND Tbls.dropped <> 'YES'
AND Mv.OWNER(+) = Objs.OWNER AND Mv.CONTAINER_NAME(+) = Objs.OBJECT_NAME
AND Objs.owner IN (<schema name>)
If it returns SYS_IOT_OVER_* tables, could you share a sample of index organized table ddl?