Stop Messenger App from opening at Login

Look in the System/Users & Groups/Login Items preference pane and make sure Facebook Messenger is not listed. If it is remove it.

Boot into Safe Mode according to Start up your Mac in safe mode - Apple Support and test to see if the problem persists. Reboot normally and test again.

NOTE: Safe Mode boot can take up to nearly twice as long as a normal boot as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files