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 Troubleshoot button which will highlight any known issues with it.
If the API sync is incomplete
Sometimes the limitations affect your account greatly and your imported data is incomplete. In such cases you can:
Check on your exchange transaction history what is missing and add it manually (How to add transactions manually)
Switch to a CSV import method instead (delete the API-connected wallet and recreate it using CSVs provided by the exchange)