Hiring is competitive and there could be a thousand reasons to pick another candidate over you. Maybe they had more experience, maybe they exhibited better critical thinking or some other hard-to-quantify skill, maybe they just seemed like a better fit. I'm not saying it's absolutely not about your stutter because it could be (I know I've been in situations where my stutter has prevented me from being picked for certain projects) but for the most part I don't think it's that big of a deal. Unless your field requires you to do massive amounts of public speaking or phone calls I don't know why they'd overlook strong candidate for a largely irrelevant disability.