If you follow the recommended overall solution (see CoinTracking FAQ: Different ways of managing your portfolio) then a negative FIAT value is to be expected.
Let's say you have deposited 1000 USD on Kraken and you have bought 1 BTC for 1000 USD.
If you don't enter the 1000 USD deposit, but only the trade, the result will be:
+1 BTC (= 1000 USD)
-1000 USD (= 1000 USD)
Total: 0 USD
The USD value will be negative because you have spent that amount for your coins.
It is not the current amount of USD displayed in your exchange.
We are recommending this method, as it shows the total expenses used to buy your coins.
Let's say you are selling your BTC later on for 1650 USD
The new result will be:
Total: 650 USD
As you can see, the total value is always the difference between income and expenditure.
So your negative FIAT amount will be what you have invested into coins minus the gains you have realized in FIAT.
If this throws you off, you can enter your FIAT deposits for the exchanges manually. Some customers prefer this method (to avoid the ugly red bar under FIAT) although we do not recommend it for reasons stated in the FAQs (see above).