Is my brother's money from his work lawful if his manager raises the price and takes the difference for his personal benefit without the knowledge of the company's superiors?

What the manager does — lying and unlawfully devouring people's wealth — is forbidden (haram). Your brother must advise him and clarify the prohibition of his actions, and he must inform the company's superiors about it. As for your brother's work, it is permissible (mubah) because he is hired for a permissible task. However, he is not allowed to assist the manager in what he does, and if he receives money from him, he must return it to the company because he would be considered a betrayer.