I've had the same trouble with Mint and started fixing it this way: click on the edit button under the item you're fixing (when you're on transactions). when the larger box pops up, in the bottom left corner there's an option to check called "duplicate". In my case, Mint was showing me all purchases on my mileage card, then recorded the payment from my bank account when I paid it off each month, then recorded the amount when it paid off the card. I just typed in the name of each transaction in the search, selected all, hit "duplicate" for all, and got a years worth fixed in less than a minute.
Still a pain, yes? ;)