I think I found a fix for this so YouTube links don't open in a popup unless it's an actual video.
In line 975 of the coherence/js/avia.js file, change this:
autolinkElements: 'a[rel^="prettyPhoto"], a[rel^="lightbox"], a[href$=jpg], a[href$=png], a[href$=gif], a[href$=jpeg], a[href$=".mov"] , a[href$=".swf"] , a[href*="vimeo.com"] , a[href*="youtube.com"] , a[href*="screenr.com"]'
To this...
autolinkElements: 'a[rel^="prettyPhoto"], a[rel^="lightbox"], a[href$=jpg], a[href$=png], a[href$=gif], a[href$=jpeg], a[href$=".mov"] , a[href$=".swf"] , a[href*="vimeo.com"] , a[href*="youtube.com/watch"] , a[href*="screenr.com"]'
Now you can enter a YouTube PAGE URL in the Coherence social media configuration menu and it will NOT be shown in a popup or give you an error, as in: http://www.youtube.com/user/GIIVideo
IF you want a YouTube video to open in a popup, then you enter the WATCH URL, as in: http://www.youtube.com/watch?v=ebmsFmSe654
I don't know if this will adversely affect any other YouTube / Popup functionality, but it's working for the YouTube social media icon.