You see this all the time with ADFS especially when setting up new Claims Provider trusts.
ADFS won't accept the metadata if the certificate isn't trusted.
Normally, you just click on the "Security Report" icon in the bar at the top of IE, then "View Certificate", then "Install Certificate".
The "Install Certificate" button won't show if you are not running as Administrator.
But in Server 2012, IE 11, I could not get the button to appear.
Mr. Google to the rescue and it turns out you have to add the site to "Trusted Sites", restart IE and then it magically appears.