All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger. We ask Allaah to exalt his mention as well as that of his family and all his companions.
If the situation is as you mentioned that the governmental company with which you signed the contract referred you to another company to get the grant for your studies according to the terms of the contract, and this referral is correct and met the conditions, and since the company to which you were referred has paid you what the local governmental company owes you, then it is not permissible for you to ask your company to pay you what is mentioned in the contract since you have already taken that money from the company to which it referred you, as you mentioned. Given that the company to which you were referred paid you, then this exempts asking your company which referred you to it from paying you again.
Allaah Knows best.