Your account balance can be negative in the following cases,

1. Daily marked to market (M2M) losses - When you have futures positions, the losses for the same are settled daily. This is reduced from your free cash balance (This is not reduced from your SPAN and Exposure margins)
2. The collateral margin received by pledging securities isn’t added to your funds statement. So when you’ve utilized collateral for taking positions, your ledger might show a negative balance.

For example, say the opening balance as per your ledger is Rs. 1000 and you have collateral margin from stocks worth another Rs. 1000. You will be able to take a position that requires a margin of up to Rs. 2000. When you take this position, Rs. 2000 will be debited on the ledger at the end of the day and your ledger balance will change to -1000.