This can be anywhere in the process from prototype to programming to submission to marketing to customer feedback.
I'm just cargo-culting the whole thing by following the instructions on the developer site.
However, the new process in XCode4 seems to have solved the problem.
My other major pain is the app review process, mostly due to a short-tempered, impatient ex-boss I must add, but the waits can be horrendous. I can wait a week to be rejected over a 10 second fix that then takes a further week to get in. Alas, no one but Apple can help with this one.
Oh - and one that hopefully doesn't apply to many others: we had a particularly vicious competitor who rallied his chums and gave our apps 1 star reviews. They even used their real names. That didn't help much!
Changes to xcode breaking the apps plists on submission is perhaps the only other grumble.