Oh prototypes. We love them, clients love them, users love them. They help with requirements and sometimes help us answer architecturally significant questions.
But early success creates a false sense of security. A successful prototype that a senior manager or a customer loves cannot always be operationalized in a matter of days or weeks. If fundamental quality attributes of software have not been thought through (e.g. security, scalability, performance, etc.) it's impossible to add that on later.
Solution? Manage the expectations of your audience. Explain the limitations before they see a demo - and discuss next steps right after prototype presentation.
Developing software intensive solutions without thinking through architecture is like taking an airplane into the air. Anyone can take off, but only pilots can land.