I don't know why it happened with your case but I do know thta often vouchers are only available for certain types of purchases. There are often restrictions on them.
For example, there may be a minimum purchase before the voucher can be used or sometimes it is only available for certain categories of items. They also have an expiry date.
Have a look at the voucher and read the terms & conditions, see if there is anything that would have caused your problem.
It is true that ebay can finish their special offers any time they like but it would be unusual I think for you to start a normal purchase and have the voucher cut out before you bought.
In an auction situation though, that could happen as the auction bids may have been spread over several days.
Have another look at the expiry date of the voucher. It may be it was valid when you first bid but expired before the end of auction.
