I'm not a web design professional, but they appear to have used it 3 ways-- 1) hosting and URL; 2) GitHub logo/branding on the footer and 3) back office collaboration tool.
I suspect it was uses #1 and #2 that generated the confusion, and while I am sympathetic to their feelings about the competition and DQ, I too might have been confused about whether they leveraged a "Wix-like" function to generate the page.
To you and me it seems obvious, but to someone less familiar the rules clearly say using Github is prohibited, even if it is for the wrong reasons. At that point you should either get clarification of the rules, or take the risk and end up in the situation OP is in now.
I suspect it was uses #1 and #2 that generated the confusion, and while I am sympathetic to their feelings about the competition and DQ, I too might have been confused about whether they leveraged a "Wix-like" function to generate the page.