All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
If this company's primary activity is permissible, but some of its activities involve what is forbidden, such as assisting in what is forbidden, then it is permissible for you to work with this company as long as your work is limited to its permissible activities. In that case, your earnings would be considered halal (lawful).
And it does not harm you that the company deals with some clients who engage in forbidden activities in Islam, as long as you are not assisting in those forbidden activities.
Allah knows best.