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Individual states run a higher margin of error due to the smaller sample sizes. In 2016 they were compounded by the October surprise of Comey’s announcement which reopened the email investigation and probably affected Clinton’s turnout. The overall decline in Clinton’s popularity dropped several points to about 3% before election day using that day’s data only. (She won by 2%). Many of the polls collected by FiveThirtyEight overestimated Clinton (or underestimated Trump) in key states and many others.
Whatever mistakes that were made in the Nov 16 elections were somewhat corrected prior to the Nov 18 elections which gave the Democrats an 8-pt lead in the polls.