If your car has broken down and is towed by recovery can you are liable to pay the toll charges of Rs 90 

The car had to cross the toll and therefore the toll has been deducted. Therefore there is nothing wrong in it.

The toll tax is payable for any vehicle that is passing through the toll gate. 

Since you have the fast tag sticker attached to the vehicle which has been towed down, the deduction was automatic.

If you want to claim back the amount, you can write to the authorities about it mentioning that it was a single vehicle which took your vehicle hence only one toll tax is liable to be paid and not double.

You can issue a legal notice in this regard and if you feel it is worth enough you can pursue the matter through consumer forum 

It's not correct as toll can be deducted only from the vehicle which is towing it not both the vehicles. You can seek refund by informing the authority

Dear Client,

                   A car owner can claim compensation from the towing operator if his vehicle is damaged, the Bombay high court had ruled in an order nine years ago. The court had then ordered sweeping changes in norms to tow away vehicles, including a rule that required the police constable to give a written order to disengage gear or handbrake to tow a vehicle away.The towing company will typically be responsible for any damages they caused; however, you or your mechanic will need to provide proof that towing the vehicle caused the damage.If you’re able to do that, the towing company will likely accept liability for the damages.You may also be able to file a claim with your car insurance company. Depending on the coverage you have, the damage may be covered.

Thanks & Regards