Group layers are useful in map services and show up in other applications. The warning message about them in the Server logs fills up the log file and makes it hard to read when there is nothing to be done about the error, and the groups are in the services for other reasons. Please remove the warning entirely or move it to the verbose or debug level or have a setting where you can select if you want to see the warning. It creates a lot of lines to sort through for little to no benefit.