Is a bus provided to staff on a contract basis or owned by the company? If it is on contract, then at the time of entering into the contract, certain clauses are enacted, and one of them should be related to late coming and the penalty for such incidents. You bluntly charge for such incidents.
If it is managed and run by the company, and the driver is on a contract basis, frequently arriving late on the premises, then at the first instance, you deduct one day's wages to avert his behavior. If it is repeated, then you can change the driver, of course, without giving more thought to it.
Regards,
Raj