Polling problems were reported in Pennsylvania, including a voting machine that registered for Mitt Romney even when the button for Barack Obama was pressed.
A state spokesman said the voter told elections officials of the problem. Video of the glitch was widely viewed on YouTube.
Officials said the voting machine was recalibrated and returned to service.
Pennsylvania was also the scene of confusion over voter ID requirements. The state this year enacted a new photo ID law but it was put on hold for the election by a judge amid concern many voters would not be able to comply on time.
Barry Kauffman of the public rights group Common Cause said election workers in many places were demanding IDs even though they are not required. It was unclear, however, just how many voters may have been turned away or discouraged.
In Virginia and Texas some voters waited in line for four hours. Recorded calls went out to residents of Florida saying misleadingly that they had until 7 pm "tomorrow" to vote.
And in Ohio, there seemed to be an unusually high number of provisional ballots, causing concern that they might not all get counted.
Election day had its share of flaws and partisan disputes but it was unclear whether any would cause a major shift in the result or set the stage for a big lawsuit. A judge in Galveston, Tex., ordered polls to stay open a bit late because of crowds, and there were court orders in Pennsylvania barring observers from interfering with voters.
Still, the day was largely uninterrupted by judicial activity.
Legal action might follow later, once margins of victory in swing states were clearer. As for election day itself, the lack of court activity may have been because both Democrats and Republicans had trained and planned for months and were out in force watching poll workers - and each other.
Liberal non-partisan groups, gathered into an alliance called Election Protection, said they received more than 80,000 calls to their hot line seeking help from confused voters. The alliance, organized by the Lawyers Committee for Civil Rights Under Law, had 5,000 lawyer volunteers in the field and 2,000 people on phones in 28 call centers in 80 jurisdictions.
One of their biggest concerns was the apparently large number of provisional ballots given to voters in Ohio, the state many consider the central battleground for the presidential election. Provisional ballots are given when information presented by the voter does not match the registration roll or insufficient identification is presented.
By law, provisional ballots must be counted if officials later determine the voter is legitimate. Many provisional ballots end up not getting counted.
At the Mother of Christ Church in Cincinnati, there was frustration among those advised to use such ballots."I don't want to vote provisionally - I want to vote for real," Canessa Harrell (42) told poll workers.
Ms Harrell said poll workers at another precinct had told her to come to Mother of Christ Church to vote, but when she arrived there, she was not listed in the rolls for the precinct.
"Will my vote count?" she asked."It will still count," said a worker, following Ms Harrell, who had decided to leave instead.