Is it obligatory to pay the additional amount to the agent upon return, given that he did not adhere to the initial agreement of providing a double room in Mecca, while a friend obtained a double room without paying any additional amount?

If an agreement was made between you and the intermediary that the additional cost (40.0) is for accommodation in a double room for the "duration of your travel in the Holy Lands," then the intermediary must fulfill that, based on the words of Allah Almighty: (O you who have believed, fulfill [all] contracts) [Al-Ma'idah/1], and the words of the Prophet, peace and blessings be upon him: (Muslims are bound by their conditions). It is not permissible for him to demand an additional fee or claim that the amount is only for accommodation in Medina, as long as the agreement covered the entire duration of the travel. What matters is the wording of the agreement. If you are certain that the agreement was for the entire duration of the travel (Medina and Mecca), then you are not obliged to pay any money other than what you have already paid.