Here are a few common reasons why you could be charged with a penalty:
On occasions, the exchange margin requirement increases after you have taken the position, more often with an options short position.
Another reason is change in security margin valuation that’s based on the price movement after you have created a position.
The exchange keeps changing the VaR on stocks that could result in change in the haircut of the stocks pledged.
Finally, shortfalls could also arise because of the MTM on your position.