All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah and that Muhammad is His slave and Messenger.
If the duties of the employee in this company are lawful and do not involve any direct engagement in prohibited acts or helping others to engage in them, then there is no harm for him to work in this company. The fact that some prohibited acts are committed in the company does not affect the permissibility of working in it (unless he is directly involved in prohibited activities). This does not contradict the prohibition of working in institutions whose activities are mostly prohibited such as usurious banks, commercial insurance companies, gambling casinos, wineries, and the like because working in such institutions entail direct involvement in prohibited acts and helping others to commit them. Allaah, The Exalted, says (what means): {And cooperate in righteousness and piety, but do not cooperate in sin and aggression.} [Quran 5:2]
Nevertheless, if the company's activities are permissible but it may engage in some forbidden activities as well, like many of the commercial and industrial companies, restaurants and the like, then the basic principle is that it is permissible for the Muslim to work in this company even if some of its activities are forbidden, provided that his work does not directly involve engaging in any prohibited acts or helping others to engage in them.
Allaah knows best.