The fav icon shows perfectly after temporarily deactivating all the plugins. It is because sometimes the plugin overwrite the theme function due to incompatibility and create conflicts.
Please follow the steps below;
1. Go to Dashboard>>plugins select all the plugins and temporarily deactivate them
2. Try reloading your website even by logging out from admin, you can clearly notice the fav icon in the browser tab. It shows there is a conflict associated with your installed third party plugin/s
3. To check which plugin/s is creating the conflict try reloading your website by activating/deactivating the plugin one by one.