I made a mistake on my return and I’m confused.

When I filed my return, I entered much more estimated tax than was actually paid.  I misread my spouse‘s handwriting and entered $7250, instead of $2500.  I had no idea that I made this error until I received a letter from the IRS, informing me that they had corrected the return.  Before the IRS caught the error, we were going to receive an $1100 refund.  They are now saying that we owe $3588.  I wanted to double check this figure, so I went back into TurbotTax and corrected the estimated taxes paid, but Turbo Tax says we owe $4700.  I’m trying to figure out if I should pay the $3588, that the IRS says we owe, or if I should file an amended return and pay the $4700 that Turbo Tax says we owe.  I don’t know why there is such a discrepancy between TurboTax and the IRS.