You probably did. The 25% you paid was only withholding, an
estimate of the tax due. No piece of income is taxed individually. All
your income, including the enlistment bonus, is added together at tax
filing time. The tax is calculated on that total (after adjustments,
deductions, exemptions and credits). Then withholding is subtracted to
determine if you owe more or get a refund.
Just verify that the 25% withheld was included on line 64 of form 1040 (line 40 of form 1040A or line 7 of 1040EZ)
