You transferred 2000 yen too much for your academic fees.
文脈と言いたいニュアンスによって、言うことが変わります。
もし話題が既に学費のことになっている場合、単に
You overpaid by 2000 yen (2000円で払いすぎた)と言います。
もし支払い方法を強調すると、You transferred 2000 yen too much
payの場合はoverpayと言えますが、transferの場合はover transferはあまり言いません。
もし学費を強調すると、後で「for your academic fees」を言います。
You paid 2000 yen too much for your academic fees
You overpaid by 2000 yen for your academic fees
You paid 2000 yen too much
You overpaid by 2000 yen
You transferred 2000 yen too much for your academic fees
You transferred 2000 yen too much