What is the Shar’i ruling on circumventing the condition "housing allowance for a maximum of three months" mentioned in the contract, given that the employee feels wronged and that this condition is not applied to some of his colleagues?

If there is an agreement or a customary practice with the company that the housing allowance is paid according to the actual amount spent, then it is not permissible to resort to trickery to take more than what is due. However, if there is no such agreement or customary practice, and the housing allowance is in exchange for your entitlement to housing from the company, then it is your property. You may use part of it for housing and keep the rest. If a stratagem is necessary to claim your right, then there is no harm in that.