How silly. I had a £12 off voucher from them which I used in an online shop. It did say that it couldn't be used for the "buy 6 bottles of wine, get 25% off" promotion, but it was refused when I ordered one of the bottles included in the promotion, even though I didn't, of course, get the discount. It's easy enough to change an item for something else when you're sitting at your computer at home, but as you say, not so convenient when you're at the till with a queue behind you.
Definitely follow it up, via the email address or telephone number on their website. It's a system error, and the store manager might have no say in the matter, but someone somewhere has made a mistake.