I think it's a matter of semantics here.
My guess is Apple already made the decision to go with Sapphire, and production had started. GT makes the rough Sapphire covers, and that sapphire would have to be polished down, and that curve on the side of the displays in the iPhone 6/Plus would have to be made, by contracted assemblers and finishers, probably at Foxconn.
The assemblers then started seeing yield and quality issues and probably had trouble grinding down the edges to make that curve, without cracking or shattering a whole lot of the sapphire covers.
To solve that issue with either a reformulation of the sapphire cover, or a different finishing process, would've taken "weeks," and Apple didn't want to wait weeks. Searching for options, Tim Cook places a call to Corning, who
maybe rubs it in and then says that they can start rolling "ion strengthened glass" (which could be Gorilla Glass 3) immediately. For a price.
End result? Apple says "sorry, maybe next time" to GT, and places a huge order with Corning for the 6/Plus. Production continues with only a minor hiccup, and GT is left holding the bag.
Again, this is all speculation, but I think this is how it went down, and how the "weeks away" rumor started.