Is the money received by the applicant in exchange for registering incomplete food quantities as complete considered unlawful money that he is permitted to consume, and must he dispose of it?

Withholding the specified quantities and short-changing the rightful recipients is a reprehensible act (munkar) that must be changed by hand; if you are unable, then by tongue; if you are unable, then by heart, and that is the weakest of faith. You must strive to change this reprehensible act to the best of your ability, even if it means informing higher authorities. Any bonuses you receive that you know for certain, or strongly believe, are deductions from the rights of the weak, you are not permitted to benefit from them, and you must disburse them to the poor and needy. However, there is no harm in you benefiting from your salary for your lawful work, as well as any reward or bonus you know does not originate from oppressing those needy people.