To be honest same question applies for any of Koinly’s alerts.
For example, my calculated BTC balance is off from my API-reported balance by a tiny amount. I just want to “accept” the alert and not have it show up on my dashboard indefinitely.
You can ignore these warnings if you find the errors insignificant. Other than that, you can manually add a deposit of the missing amount to remove the errors.
How to add transactions manually