Is the increase in the money she returned to her sister considered usury, knowing that she intended the increase to be charity for her?

This increase is not usury (riba); rather, it falls under theحسن القضاء (excellent repayment/settlement), based on the Prophet Muhammad's (peace be upon him) saying: "May Allah have mercy upon a servant who is lenient when he sells, lenient when he buys, lenient when he settles a debt, and lenient when he demands repayment." It is desirable for the debtor to repay generously as a reward for the creditor and in emulation of the Prophet (peace be upon him), who repaid better than what he borrowed. Therefore, your kindness to your sister and your payment to her of more than her due is permissible.