I have to think Apple had done some due diligence of the suitability of sapphire for their needs before committing all the money to loan to GT to build the factory, and bought all the furnaces they equipped it with. They will have worked out all the production issues before making an investment of that size, but there are a lot of steps after proving something will work to proving something will work in 150 million devices a year.
I'll bet it was either GT not delivering on their end, or possibly it isn't hard to cut the screens in small numbers but making them by the tens of millions has proven to be problematic so far. Sapphire is very hard, after all, so you pretty much need to use diamond coated tools or lasers to cut it.
Maybe Apple couldn't source enough of those tools in time to produce the screens at a high enough rate to be used in the iPhone 6. That might be where the August rumors of "sapphire will only be for the 6 plus" or "sapphire will only be for the 128GB version" came from, if rumors were based on some truth that Apple was considering whether to try to make due with a severely restricted supply.
I'm imagine it'll probably come out in the bankruptcy hearing, or shareholder suits against GTAT management.