There are some countries that don't allow photography over their air space. As one who loves taking pictures from the flight deck I know that Russia and Belgium don't permit this. I can't imagine how it's enforced but a quick google search uncovered this:
http://europa.eu/rapid/pressReleases...guiLanguage=en
Yeah it's old I know, but I suppose this could be the reason that some crew have prevented others from taking photos?