What is the ruling on working for a company that facilitates investment, knowing that some of the stocks traded are not compliant with Islamic Sharia?

It is permissible to trade only in lawful stocks. It is not permissible to cooperate in sin and aggression. Therefore, if your work involves facilitating the purchase of prohibited stocks in any way, then this assistance is forbidden, and the resulting salary is unlawful. You must strive to leave this company or transfer to a department free from prohibited transactions.