Github pages allows you to write index.md instead of an index.html, and therefore they count it as a webpage generator. Not sure if these kids used a markdown file for a page, but the capability is there and that makes Github more than just a dumb web server that serves html.
Possibly the judges are non technical, just basic designers so they can't tell the difference, so all Github pages would be banned and not just the markdown ones. But I think it would be better if they told the students so they could move it to a clean server in that case.