In wordpress plugin or theme settings API, when we add settings error, I face problem with display update message twice. and this is happen only when first times settings save.
After a day long troubleshooting, I got this is because when update_option, it call add_option function first time. and that is the main reason to display update message duplicate in first time save.
To resolve this issues, I added default options value by update_option when plugin is active and error gone!!!
Hope this help others.