While the question is old, I had the same problem and finally got it resolved through AppleCare. I'll share what I learned in case it can be of value to anyone else.
(In fact, I actually had additional problems, including Time Capsule suddenly failing to do backups for a 3rd computer. I'll list everything I can remember in case it helps.)
1) I unplugged my Time Capsule for one minute for it to reset. This allowed regular backups to resume for the 3rd computer.
2) In Finder, I found the backups on Time Capsule and double-clicked the one I couldn't open in Migration Assistant. This doesn't do anything obvious, but the AppleCare assistant said something about making it the default for Migration Assistant.
3) In Migration Assistant, I got to a window asking me which system to migrate from. Instead of selecting what seemed like the obvious choice (my backup file under Time Capsule), I needed to select "My Macintosh HD".
It finally worked for me. If the above doesn't help, I suggest you call AppleCare (you automatically get 90 days of AppleCare with a new or refurbished machine, which is great if you're having trouble with Migration Assistant, because you probably have a new machine!)