Is there an Islamic accountability for employees in a car company if their incentives are partially based on the profits of a department that deals with customers who have Sharia-prohibited car insurance, knowing that this department also deals with customers who do not have insurance?

There is no blame upon you for what your company earns from repairing cars for those contracted with insurance companies, whether the insurance is permissible or forbidden. The customers pay the repair costs from their own money, and you have no relation to what they recover from the insurance company. And even if they paid from forbidden insurance money, the preponderant opinion is that there is no blame upon you; because money forbidden in its earning, its sin is upon the earner only, not upon whoever takes it through a permissible means, unlike what is forbidden in its essence, such as alcohol and usurped property. This is supported by the Prophet's (peace be upon him) dealings with the Jews and their consumption of usury.