Might this be an instance where prediction markets greatly out-performed the experts? In short, no. There were relevant markets but two big problems:
No one thought to create a market for the number of flu cases over a couple of thousand.
Prediction markets require a verifiable outcome so they were based on CDC confirmed cases. But after the flu turned out not to be that dangerous, the CDC stopped confirming most cases and there were less than 7500 confirmed cases by the end of May.