I have this persistent WARNING, too. Mine is limiting the query results to 6. This WARNING is always accompanied by a separate SEVERE message stating "General geodatabase error occured." (sic).
My feature service has two layers and a table, which are all from the same database and are all related using relationship classes in the geodatabase.
To be clear, the rest service URLs for each layer all show that the max record count is set to 1000.
ESRI has attempted to help me troubleshoot this, but could not find a recommendation other than to upgrade our server. We did this: from SQL Server 2012 to 2016, plus ESRI professional services deployed a new, separate web server for us that has been upgraded to Enterprise 10.6.1. Both have had their memory and RAM increased. We are now using Portal instead of ArcGIS Online.
And yet, this issue persists on our most important feature service.