Is there a sin upon one who benefited from company food and food allowance together, despite knowing the impermissibility of combining them, and his intention was not to defraud?

If the company prohibits combining food with its substitute, then it is forbidden to combine them. If you agree with the company to eat, you must return the food allowance to the company, even indirectly. And if you agree to take the substitute, you must return the value of the food to the company, unless the company absolves you of it.