Allegedly, votes have been stored incorrectly, some booths did not provide absentee ballot papers, and some people were marked off electoral rolls as voting when they could not.
The claims come from three different states.
The Australian Electoral Commission is facing a series of complaints, and the situation could even lead to a challenge in the currently undecided West Australian seat of Cowan.
Hundreds of votes in the seat have allegedly been stored incorrectly and not properly signed by a returning officer.
Those complaints come as independent candidate Rob Oakeshott has lodged a complaint with the commission over the redrawn New South Wales seat of Lyne.
He says voting officers there ran out of Cowper absentee-ballot papers on election day.
The seats of Lyne and Cowper had been extensively redrawn as part of federal redistribution, meaning voters who used to be in Lyne had to ask for Cowper ballot papers at their local booths.
Mr Oakeshott, who retired as the MP for Lyne in 2013, challenged Coalition MP Luke Hartsuyker in the redistributed seat.
He says voters were also told they would be signed off the electoral roll but were not able to cast a ballot.
Luke Hartsuyker says it is a matter for Mr Oakeshott to address but he does not imagine it will affect the result.
"Well, that's very much a question for Mr Oakeshott, but certainly the results as have come in so far show a very strong return by myself, some support for Mr Oakeshott, but nowhere near enough to get him over the line. We're in a very strong position, and I think that there is no way that a recount could yield another result."
Meanwhile, Queensland senator Glenn Lazarus is seeking legal advice about the validity of the election after receiving reports ballot papers were in short supply at polling booths.
Senator Lazarus, who has conceded defeat in the state's Senate race, has questioned the processing of the election.
The former Palmer United senator says he received many complaints about people being marked as having voted despite polling booths running short of ballot papers.
"Oh, look, we've just been inundated with emails and comments on Facebook about the fact that people have turned up to polling booths, not only in Queensland but in other areas, had their names marked off the roll, but weren't able to vote because there were just no ballot papers. But they were told that they would have their names marked off the roll just so they wouldn't receive a fine, and that was it."
The Electoral Commission's Phil Diak says all complaints are looked at after the election.
Mr Diak has told the ABC the vast majority of people did not experience problems with voting.
(Diak:) "It's hard to comment with a view, if you like, across all of the booths when the vast majority of 9 million people had a satisfactory vote in a calm manner and exercised their franchise on election day."
(Question:) "But would that be legal?"
(Diak:) "Well, I wouldn't like to hypothesise on any of those matters that have been reported, including by Mr Lazarus. All of those matters will be looked at as part of a post-election review. At the moment, our focus is on doing a count in a correct and careful manner, and that's what we're about at this stage."
Mr Diak has conceded electronic voting could be a way to solve any voting problems.
But he says that is a decision for federal parliament, not the commission.
The ABC's veteran election analyst, Antony Green, says he, too, thinks electronic voting could help.
"But what you could do in the largest polling places is to do electronic absent voting, so that, if you're not from that district, (if) you're from another district, there are computers available for absent voting. Much of the paperwork problem in polling places is to do with absent votes. And most of the concerns you've heard about with missing ballot papers, not having ballot papers, is to do with absent votes. And some of the polling places seem to have run out of them."
In 2014, West Australian voters were forced return to the polls after the High Court ruled the September 7 election result for the Senate that year was absolutely void.
The finding came after an electoral debacle involving two full recounts for the Senate and the loss of 1,370 ballot papers by the Australian Electoral Commission.
