I've had a similar problem with the Prometheus Blu-ray's digital copy and itunes extras. Now I also have this problem with Star Trek Into Darkness and its digital copy.
Last time it happened I emailed Apple who gave me a very standard and useless 'try redownloading it now, we have readded it to your account again'.
I had the extact same problem.
In the end the problem just sort of fixed itself. I left it for a while figuring I had tried what they recommended and couldn't be bothered anymore. Then after a week or so I thought I'd give it another go and it downloaded fine, and at a much quicker pace too.
I recommend patience, as Apple will be no help whatsoever, and I reckon in a week or two the downloads will probably suddenly work fine.