You're not alone. Mine does this too. Did it ever since having 13 miles on it. Now it has close to 500. Mine also has developed this moaning/whine noise that occurs after exceeding 30 mph. It's always actually done that, but was told today by a tech (not a trans tech, though) that it is more than likely a trnasmission problem, and may be a simple re-programming fix.
At least, if shuttering what the only thing it was doing, it may just need to be reprogrammed, which I've read a few stories (of people having to do) online.
Anyway, I'd just take it back to the dealer and explain to them, and have a tech look at it. I will note this: you need to have a Ford certified trans tech look at it, not just anybody because it could actually affect your warranty, which is what my dealer told me. Most dealerships have certain people specialized to work on trannys, and they should be the only people performing anything relating to the transmission.
What I've also noticed with mine is that it seems to run through 2nd gear real quick. That, and I seem to hear excessive noise when it's shifting (not so much a constant noise when shifting, but more like a grinding noise like the clutches aren't engagin/disengaging completely). So, from my perspective, it seems like the car's already in 4th gear by the time it hits 30-40 mph, which might be normal, but it doesn't seem normal (or feel normal) to me. And at around 65mph, the 2012 likes to run at around 2500-2600 RPM. My 2010 Focus would only do about 2300-2400 at 70 mph, and that one had less horse power and less torque, so this is another indicater to me that something might be wrong.
But anyway, you're not alone. There are at least a few of us out there with trans problems. Hopefully Ford has a recall for this issue (it would still be covered under warranty regardless) but over time, if not treated, it could cause serious problems for when the warranty period runs out.