Please ensure you are using the "Unsold Assets as Cost Basis" setting, because "All Assets as Cost Basis" will calculate with average prices and is not recommended (read more).
Another name for cost base in Cointracking is asset value. You can adjust the asset value of a transaction by editing them via the Enter Coins page where you can search for the trade. Mark the trade and click on "Edit" and afterwards on "Edit Asset value". There you can adjust it.
A case for a necessary Asset Value/Cost Basis adjustment of a trade would be, if you bought new coin (e.g. during ICO) which was not listed on coin price sources during the purchase time. In this case please open all transactions on the Enter Coins page and enter the sale value into the empty purchase value field:
Please note that deposits and withdrawals do not have a cost basis as they are considered movements between wallets or exchanges. That's why they will not be calculated in the tax report.