If the manager said it was OK, she should have told the OP. In any store that I've worked at, if the manager overrode some policy, they'd bring the customer to the cashier and say, "Please ring this through for last week's sale price at 6.99" or "We're going to exchange this bra strap for that one even though it's a different one." Or they'd complete the transaction themselves.
By the way, customers lie about this kind of thing all the time. I used to see evidence of it constantly.