When you don't pay the fees with BNB (or you are trading a bnb pair; xxx/BNB), the commission will be subtracted from the acquired coin.
For example, let's use QTUM/BTC, the buy commission will be deducted from the QTUM obtained amount and the sell commission from the new BTC acquired amount.
Due to the Binance precision requirement, your buy amount has to be rounded down. so, you buy 300 QTUM, pay a commission of 0.3. You would have 299.7 for selling. Because the precision needs to be at 0 decimals, it would only leave you to sell 299 QTUM, leaving you with a 0.7 bag of QTUM.
If your position size is small, this could reduce your net profit considerably, even make them negative.
Take into consideration that you still would have a small balance of that asset that is not computed. Remember that you can convert your small balance to BNB.