Is food purchased with money taken from the company, then repaid later, considered unlawful?

There is no doubt that your taking from the fund's money is an aggression and a breach of trust. What is obligatory in this matter is sincere repentance. As for what you bought with this money and returned its price to the fund, it becomes permissible for you to benefit from it. So, there is no sin upon you in benefiting from what you have. Beware of returning to such a sin.