I highly doubt that Apple is upset that the last generation iPhone with its fully depreciated components is still selling well. In fact, it’s probably a boost to Apple’s profitability. If Apple could get away with selling the same phone for two years, they probably would.
Apple and the Seduction of Last Year's Chip
I would bet money that the iPhone 6 has margins that are at least the same as the current iPhone, even with the price drop. There’s a reason why Apple likes to keep older processors and products around. They are more profitable, not less. That’s why the iPad 2 stuck around for so long and why the MacBook Air is still in stores alongside the new 12” Retina MacBook. The problem isn’t with margins, it’s with falling unit volumes.
I do think that Apple’s margins could be in for a hit but not because the iPhone 6 is doing well. If there is a margin landmine buried somewhere, I’d finger the Apple Watch as the prime suspect.