The mobile previews from Origami-like tools will show a refined "golden path" through the app with beautiful stock photos in every screen, but more boring use cases tend to be ignored. This tends to lead to usability problems down the road, when users discover those "dead ends" that the design unconsciously avoided.
It's also frustrating for programmers when you are handed a high-gloss prototype that has no relation to the actual platform UI classes and guidelines. Implementing all those fancy little triggered animations takes so much time that no one has time to peek at the iOS guidelines and notice how the design actually breaks 80% of Apple's rules.
Companies like Facebook have enough resources and actual UX competence to get these things right (eventually), but I've seen this happen too many times at smaller agencies and startups.