Some exchanges do not provide Koinly with full access to your transactions even after you have added your API keys. If you have negative balances in your wallets after a sync then it could be due to such issues.
You will be able to see any API limitations when setting up a new wallet in a yellow warning such as this one:
If you have already created a wallet then you can click on your wallet and then on the Having trouble button which will highlight any known issues with it.