Is money earned from working in an office that uses pirated computer software permissible or impermissible, and what is the ruling on the money that has already been spent from it?

Using copyrighted software without the permission of its owners is not permissible. However, if your work with the company does not involve or assist in what is forbidden, then there is no harm in it, and your earnings from it are lawful. You should advise them to stop using unlicensed software.