1. Yes, you must return the extra money that you were mistakenly not charged.
2. The decisive factor in these type of questions is whether the employee of the company has the authority to give a reduction of this nature.
A supermarket cashier, for example, is probably authorized to allow you to pay 10 agorot less than the price. But to give a significant reduction would
require the permission of the manager.
The question here then is whether the bus driver is authorized to waive the extra money. I suspect that in this case he is not, and thus you would need to pay the company.
To be certain, contact the company and ask them if the driver has such authorization.