It didn't, because it only addressed Android so far:

http://europa.eu/rapid/press-release_IP-16-1492_en.htm

"At this stage, the Commission considers that Google is dominant in the markets for general internet search services, licensable smart mobile operating systems and app stores for the Android mobile operating system."

Not only the EC used "licensable smart mobile operating systems" but it also used "app stores for the Android mobile operating system".

It assumed that Android does not compete with iOS and that the Play store does not compete with the App store.

So, if Android doesn't compete with iOS, then Apple has a monopoly in it's market: proprietary non-lincesable mobile operating systems.