What exactly do you mean by "taking out money"? If you sold shares of a mutual fund (other than a money market fund) in order to get money out, you have to report the sale on your tax return. You will get a Form 1099-B from the fund showing the sale. If you sold shares at a profit, you have to pay tax on the profit. It's not a penalty, it's regular income tax on the profit from the sale. You have to pay the tax, even if you later put the same amount of money back into the fund.
