We deprecated several old URL formats for accessing core pages (this does not affect Friendly URLs). The old formats included: (1) www.domain.com/index.php?ct=site.contact, (2) www.domain.com/?ct=site.contact or (3) www.domain.com/site.contact all of these methods were very old and should not be used anymore. The correct format is www.domain.com/site/contact, and so we updated all the instances where the old method was used.
Our CMS will still correctly recognize the old formats 1 & 2, but not 3, until the next upgrade. But any pages using the old method should be updated ASAP.
If your site is getting a 404 page not found error, please send us the URL of the page that is not loading, as well as the URL of the page you were on (with a description of the link that you clicked).