The issue of being nehneh from a ness depends on whether the person was matriach es Hashem to make it. If it is something absolutely necessary like krias yam suf or the mon, the ness is a chesed and there is clearly no problem in using it. In fact, one could even prove from the ness that the ratzon Hashem is to use it. No one asked any shailos about the kashrus of the mon. Eliyahu ate from Achav's kitchen because Hashem made it happen through a ness (Chullin 5a).

However, in this case they asked for the meat wrongly, and that is why there was charon aff. When Moshe warned them against eating the meat, the people thought he was talking about meat that would come in a natural way. When they saw the slov come in a supernatural way so much of it, all flying at arm's height they said, either we were right after all for asking for it, or else we were wrong but Hashem forgave us, so this is considered a ness similar to the mon and it is allowed to be nehneh. That was their mistake.