It's a little more complicated than that. Since 1986, the law requires that any withdrawals made of after-tax monies from a qualified plan must have a proportionate amount of earnings attached to them.
Assume a participant with a $15,000 after-tax balance in her account – $10,000 of which is principal (non-taxable) and $5,000 of which is earnings (taxable). Since the $5,000 in earnings represents one-third of the overall $15,000 balance, that means that any withdrawal she takes of after-tax dollars must consist of roughly 33% in earnings. In other words, 33% of whatever withdrawal she takes will be subject to ordinary income tax AND a 10% early withdrawal penalty.
It's hard to tell what the issue is without knowing more about your return. On top of the above explanation, check if there's a difference between box 1 and box 2a and ensure the code in Box 7 is correct.
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