I think they overestimated the appeal of the iPhone 5C for the "1st day buyers" crowd.
I mean, the 5c is a great phone, love the overall design and honestly I think I would prefer the 5S having the 5C plastic casing. However, it is still the "last year phone" in a new plastic design at the same price than the iPhone 5 would have been (being the 99$ subsidized option for the year to come). Even if they market it as an all new product, peoples still see it as the "last year phone", and I think that it will eventually sell very well medium/long-term, it won't have the same appeal at launch date as the all new high tech iPhone 5S. Especially since it is not really the "cheap iPhone" we were all expecting. I know that personnally, the iPhone 5C would have been 200$ cheaper than the 5S, I would have seriously considered buying the 5c at launch instead. But for 100$ difference, the 5S seems to justify the 100$ difference easily. 200$ too, but not as clearly.
Anyway, right now every iPhone 5C is still "24h" on the Apple store, while the 5S is now delayed to simply "october".
So, I guess it didn't went like they expected. It happen, too bad. We'll live through it !