From what I've read, there's nothing wrong with the results of the Miller-Urey experiment, only whether its setup was actually similar to conditions on the early Earth. In other words, it is unlikely that Earth's original atmosphere had large amounts of methane, ammonia and hydrogen (e.g. a Jupiter-like atmosphere). More likely it consisted of elemental nitrogen (N2), carbon dioxide, and water vapor. Using a mixture like that, very few organic compounds can be created by electrical discharges.