I was using the "Custom multisite favicon" feature but it seems to be conflicting with the new Wordpress native favicon support - https://codex.wordpress.org/Creating_a_Favicon
Whenever I added the WordPress favicon to a subsite on the multisite, that favicon would not show. In "view source" on the page, I would see the WordPress-defined site favicon IN ADDITION TO the favicon defined network wide in Ultimate Branding - meaning some browsers would should one or the other - most of the time the only favicon that would show is the UB default network one.
I had to disable this feature of Ultimate Branding so that the custom WordPress supported favicons would show at all.
Could you update the plugin with a check to see if the WordPress supported favicon has been set already - and only show the UB one if the site's favicon has not been site in WordPress.