If your spouse if a full-time student, then for purposes of the calculations on the 2441, your spouse is credited with $250/month of earned income (or $3k/year).
So, on line 20, the choice is made to select the smallest of 17, 18, and 19. The $3k is one of those lines, so the amount of your expenses applied to this process is only $3k.
Therefore, since you could not show that all $5k was used for justified child care expenses, the part that was not justified was added to taxable income.
Next year, if your spouse's business makes more money than $3k, then do not report your spouse as a full-time student, but let the spouse's earned income be used instead.
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