I wonder if this is because of the situation in Israel & Palestine ?
I think I heard on Friday before Eng v Aus game at Wembley that only national flags allowed because of this. My assumption is that it's an easy way to bar/block political flags of any sort i.e. no pro Israel nor pro Palestine flags currently. Just a blanket ban apart from actual national flags of the 2 teams competing in that particular match to avoid any potential controversy.