A Fab takes several billion to set up and the reduction of the die scale (32 - 28 - 22nm) takes another couple of billion to tool up. That is why Intel are so far ahead at the moment, AMD can't afford to keep up.
For ARM, Samsung are the leaders at the moment, the others are still catching up to their current scale.
That said, Apple have been buying their ARM chips in huge quantities from Samsung. They are now looking to buy less chips and source the rest from elsewhere. If they have found somebody else to provide a portion of their chip and have reduced the number of chips ordered from Samsung for a quarter, they aren't fulfilling the agreed purchase volumes, so their discount will be less.
Without knowing the full story, it is difficult to tell exactly why they raised the prices...
On the other hand, maybe they've had to put up their prices to cover the legal costs of fighting Apple in the courts.
