I dont know why the OP couldnt have simply asked Citi to cut acheck for the duplicate amount that was sent in unless they had charges already on the CC after the statementw as closed , and which will appear on the next statement that would have been Debited as being paid due to the Auto Pay kicking in

Ive paid a CC twice from time to time and all I did was ask that they cut me a check for the amount I ended up over paying by. It might take 10 biz days till you get it but thats how most CCs work.

Sorry but I disagree with the OP if Citi has T&Cs in place for how an AutoPay must be CXed and its not followed or cant be (not enough time) then its not Citis or any Banks Fault. Now ifa person will still want to remain with that Bank is something else but it seems that the OP ran aground of Citis T&Cs and it seems they didnt even know they existed , since Im with Citi myself and most everything is always in Print Id put the burden on the OP for not knowing the T&Cs

Im sure instead of Stop Payment on either payment had they asked that a check be cut it would have solved the problem, only the check probably would have arrived when the OP had already left town, again not Citis problem sorry to say