In Marion County, around Indianapolis, the clerk said insufficient training resulted in half the 914 precincts getting a late start in voting.
In Delaware County, where Muncie is, a judge ordered polls to stay open nearly three hours later after a programming error stalled voting there.
One LaPorte County precinct had another type of problem that extended voting.
As the first voters of the day tried to cast their ballots at this Hudson Lake precinct, they found they could not.
Six machines would not accept their vote.
"We all make mistakes, but it's a little difficult to understand exactly how this particular mistake occurred," explains Robert Behler, LaPorte County Circuit Court Clerk.
LaPorte County uses a full electronic voting system.
Voters push a button to choose a name.
Before anything happens, a trained poll worker starts things up using a card. The problem was the worker used the wrong card.
"The start card to get started in the morning and check the machine; and then a vote card that's used with each voter during the day, by the precinct worker," explains Behler. "The red tally card, which is used at the end of the day to close the machine and get the vote totals, was used instead to try and open the machine. Which, in effect, told the machine the election was over don't allow any more votes."
More than 1300 people are registered at the Hudson Lake precinct. Officials do not know how many were affected by the delay.
"I did obtain a court order to stay open one hour past the regular closing time to accommodate those voters," say Behler.
For the first time in history, a judge had to order one polling place to stay open an hour later in LaPorte County.
County Clerk Behler says the poll worker used the machines back in the May primary and had received over five hours of training.
He blames the delay on nothing more than human error.