Why is this happening? The short answer is: the Invisible Hand of the market doesn't care whether you get sick.
Since the killer flu season of 1989-'90, flu outbreaks have been mild. Demand for flu shots has been declining, and, since the shots expire in June following each flu season, drug companies in each of the past five years have discarded unsold vaccine.So this year they only made 83 million, another killer flu season hit, demand increased, and they ran out.
Last year they made 95 million doses, sold 83 million, discarded 12 million.
It's a lot worse for private manufacturers to have too much vaccine than it is for them to have too little. Too much, and they're out the whole cost of the extra doses - too little, and they've lost a much smaller amount of money per dose in foregone profits. So they'll try to make enough vaccine to meet demand, but they have no particular incentive to leave a wide safety margin.
We've ceded huge swaths of our public health infrastructure in this country to private corporations, mostly on the logic that privatization is more efficient and less expensive and good for campaign donations. And as long as it only involves private organizations contracting to perform services as directed by public agencies, it apparently works reasonably well. But public health decisions simply shouldn't be based on the profit motives of private companies. As a society, we can't afford to just hope that when an epidemic strikes, the Invisible Hand will reach out and give us a syringe.
(Incidentally, watch for conservative pundits to start blaming the flu vaccine shortage on lawsuits against vaccine manufacturers and saying that we need tort reform to protect us from future shortages. No matter what problem faces America, the answer is always one of these three things: tax cuts, "tort reform," and drilling in the Arctic National Wildlife Refuge.)