I found something interresting in their FAQ:
https://cointracking.freshdesk.com/en/support/solutions/articles/29000018276-missing-fees-in-the-tax-report

Missing Fees in the Tax-Report
Modified on: Wed, 6 Dec, 2017 at 10:04 AM
"At the moment, the fee values are not deducted from your gains in the Tax-Report.
You can easily find them on the "Trading Fees" page and subtract them yourself from your total."

If I substract my fees my gains now appear to be underestimated by CT, but not by much. 

Dario can you tell us if this FAQ is accurate and we must all substract our fees from the gains in the Tax report?