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IRS Direct Pay and Efiled tax return

A taxpayer made a tax payment using IRS Direct Pay before the tax return was efiled.  The tax return submission was rejected.  The diagnostic says that tax return was rejected because the ssn on the tax return was used on a previously efiled tax return.  Is it possible that the tax return was rejected because the payment made via IRS Direct Pay was done before the tax return was efiled?  Please let me know what you think.  Thanks