I haven't seen demand numbers, but it does seem that Apple underestimated the demand. My guess -- which is pure conjecture -- is that Apple ordered fewer iPhones than usual this year because it expected to take a hit based on the non-inclusion of the headphone jack and because it was making relatively minor external changes for a non-S year. I'm further guessing that Apple allowed the early leaks with respect to the headphone jack so buyers would have time to absorb the news (rather than being hit by surprise with bad news at the keynote). And, somewhat to everyone's surprise, the under-the-hood improvements really amounted to something. When you combine those factors with the Samsung debacle, that's a formula for higher-than-expected demand.
Also relevant is the apparent fact, based on a fair bit of anecdotal evidence from the field, that a higher percentage of people are opting for the 7 Plus this time, as opposed to the prior percentage. I'm guessing that Apple is seriously scrambling right now to catch up with demand.