Is it permissible to set aside the portion of a salary, earned from working in a company whose products include some that are questionable or unlawful (haram), and spend it on purchasing necessities and supplies specifically for the company, such as tools or phone recharge cards?

If your work in the company is free from direct involvement in haraam (unlawful acts) or assisting in it, then there is no harm for you in the salary, and you are not obliged to give anything out of it. This is because the company's wealth is mixed, and we have explained the permissibility of dealing with someone whose wealth is mixed. However, if some of your work is haraam, then you must give out the percentage of the haraam from your salary to the poor or for charitable causes and public benefits for Muslims. It is not permissible to spend it for your own benefit or for the benefit of your company.