i can understand the withholding shown on the 1099. you state "plus more deducted when I did the amended return" This does not seem possible, so could you please clarify this.
on an early withdrawal of $2,600 you would owe a penalty of 10% or $260. in addition you would owe ordinary income taxes less what was withheld. in addition there would be late payment penalties and interest if you file the amended return after 4/15/19
we can't see your return or amended return so we can't say if additional income would affect other items on your return such as credits, itemized deductions, etc.
it is entirely possible you are right and the IRS made an error when process the 1040-X. however, 1st i would check the submitted return to make sure everything is correct. next I would download a transcript of the return from the IRS website and compare it to the 1040-X to verify that it is an IRS error rather than an entry error you made.
