You register in a class, here in the UK FaceTime wasn't registered until this March. It's registered against the Nice Classificiation (http://www.wipo.int/classifications/nivilo/nice/index.htm?la...) meaning that if you want to use the term FaceTime for anything encompassed by classes 16 or 35 then you need to license the trademark.
Apple are an international company and need to abide by trademark restrictions in other jurisdictions in which they are operating commercially.
FaceTime appears to have been registered using the Madrid system in more places than just the US.
So, whilst the US-only classes are quite narrow this is not the end of the locus of operation and so international trademarks have to be considered.
If it was only registered in March 2010, doesn't that cause a problem for using the Madrid-system registration to enforce the trademark against products that were released in 2009, like this one? At least in the U.S., the various presumptive benefits of having a registered trademark are much weaker if you're trying to enforce it against a usage that preceded the registration. It seems they would have to rely on the older FaceTime Communications USPTO marks in order to establish priority, but those marks are only in the narrower U.S. classes.
I only did a quick search (UK, US), there could be community (EC) registered marks that are earlier but these should have shown up (in the UK search).
Trademarks are unregistered IP as well as registered. Registration gains you more protection and makes suing people easier but it can be done with an unregistered mark (or that's how things work in the EC).
It doesn't matter when any product was made in as much as the registered mark is a sign of the origin of goods/services it is not a product mark. If there is no other IP protection on your product I can rip it off and sell it as long as I don't use your trademark.
I don't know sufficient to comment on priority of registrations in the US both in the specifics and in general, sorry.
The purpose of trademark law is to prevent the public from being misled as to the origin or quality of a product or service, and to identify the commercial source of products and services. There would likely have been confusion between two apps with the same name in the App Store. Apple registered the trademark, submitter did not. It's a pretty cut and dried case.