How can a Muslim employee deal with requests from their manager that violate Sharia, and how can they avoid getting into this situation from the outset?

It is not permissible for an employee to obey superiors in matters that contravene the Sharia, based on the Prophet's (peace be upon him) saying: "There is no obedience in sin; obedience is only in what is good." The superior must be advised and reminded of Allah. If the employee can continue his work without directly engaging in what is unlawful or assisting in it, then he may remain. However, if the work requires participation in unlawful acts, it is not permissible to stay in it, and he must seek another job, for Allah has guaranteed provision and a way out for the righteous.