Cryptocurrencies that have a very low value when compared to the likes of ETH or BTC have long decimal values that are very important and significant even far after zero.
An example would be XVG. In December of 2018, 5,000 XVG was worth just 0.5 ETH.
Unfortunately, some exchanges like Binance round off these decimals rather early in the trade history file that you export. These rounding errors can add up and make it look like you are selling more of the cryptocurrency than you own when you import your CSV files into CryptoTrader.Tax.
You will likely be able to tell if your Negative Balance Warning is being caused by a rounding error if you hover over the warning icon and see that the amount of XXX coin that you own at the time is very close, but slightly less to what it says you are selling.
Currently, the CryptoTrader.Tax development team is working to build out API imports from these exchanges so that these rounding errors don't occur.
A temporary fix is to add an "Incoming Transaction" on Step 3 of the app using the currency that is giving the error.
For example, if the Negative Balance Warning says you are attempting to sell more XVG than you own at the time of the trade and the amount you are selling is 4997, yet the amount that you own is 4994, then you should add an Incoming Transaction of "3 XVG" at a date prior to when you were selling this coin. Then click Save.
This will eliminate your Negative Balance Warning and allow your report to run completely.
This fix will have little to no effect on your true tax position as long as you add enough of the coin just to fix the rounding error.