Is it permissible for an employee to keep an excess amount of money previously sent to him by the manager, which was not deducted by the accounting department, especially after the manager's departure? And what should he do with this amount if he is not entitled to keep it?

It is possible that the amount paid by the manager was from his personal money or from the company's money. Therefore, he must be asked about its source to determine who is entitled to it. If it is not possible to ask him, and the company refuses to receive it, then it is permissible to give it to the poor and needy, based on the saying of Sheikh al-Islam Ibn Taymiyyah that any money whose owner is unknown should be given in charity and spent on the welfare of Muslims.