In financial world, a negative balance indicates credit on company. Before this the balance you used to see was actually wrong. The amount you recharge becomes a debt on company. Hence negative sign. The balance you owe to them is positive. The negative balance tells you that this is amount company owes you. My balance is shown negative since last August on website. They updated in app now.
Moreover, if you are on annual pack that has offer balance then on website you will get different balance from app. Like in my case my annual pack is till 22/12/2019. On App it shows balance as -3519 and website -4471 as it has offer balance of rest amount of 952. If I change my pack now to new regime, this 952 will be deducted and rest 3519 will be available to me. So they have actually corrected everything now.