Can you look at both instances of the transactions (the original one and the duplicate) and see if any are displayed as “pending” when you scroll all the way down on the transaction detail screen, and if so, you might even be able to reverse those yourself by tapping the “something’s wrong” and following the instructions (do it only on the earliest instance, as we assume the later instance is the “correct” one that will get settled).
It could be that the merchant has authorised the first transaction (which temporarily locks the money away, on a legacy bank it would reduce your “available balance” but Monzo displays them as if they were settled transactions for simplicity) but instead of just settling it they submitted a second one and will not be settling the original one (eventually it will expire after 10 days, on Monzo it’ll show as a refund even though technically the money has never been taken to begin with).
Keep in mind that you will only be charged overdraft fees on actual, settled transactions. You will not incur any fees even if pending transactions appear to have taken you into overdraft.