I figured out the issue. In my plugin I was calling an echo statement from a WP_Head function. This was causing the <head> tag to be immediately closed and rendered in the body. Any remaining code for the WP_Head was being output in the body, including the favicon <link> tags.
Triggering a timewall after X days
Why sometimes wp_redirect() reset cookie?
Log in user using WordPress REST API
Even if this plugin isn’t updated, I use it and it works like a charm: https://wordpress.org/plugins/wordpress-mu-domain-mapping/
This fails because the init hook is far too early to call is_page_template. Conditionals such as this function use the main query to decide their value, but WordPress hasn’t created the main query yet. The earliest hook you can safely do this is template_redirect.
Codeless random token generation to pass into multiple tracking links in a single page load
Multisite cookies are being shared across domains unwanted
Solved: The database contained tables of tested plugins containing that cookies. Removing the old tables removes the cookies from the browser.
Is there something I need to know in order to use WordPress on foreign (Swedish) TLDs?