bottom line-- I made an estimated payment but they included it in Income tax withheld and then again in Sch 5 line 66
Wow ... and you didn't notice that error before you filed ? This is a data entry error on your end as the program could not have entered it twice by itself ... line 66 would have been entered automatically if you transferred the 2017 info into the 2018 program and you had estimated payments calculated last year. Did you also make an entry somewhere else ?
Good news is the IRS corrected the error so you don't need to amend the return HOWEVER I suggest you do amend the return so your tax file in the system is correct ( just don't mail it in) ... so this will give the the chance to see where the duplication happened.