We do not charge the trading fee upfront, meaning the fee amount is deducted after the trade is executed.
So if the balance amount is less than the trading fee amount, your fund's balance will go into negative as per the fee charged in the last trade.
For example, you have 10000 INR and want to buy BTC using the entire INR balance. You will receive the whole BTC amount and the fee amount will get deducted from the INR balance after the trade execution. As you had used the entire INR balance to buy BTC, the fee amount will go into negative, which will get settled against your future sell orders in INR markets or INR deposit.