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.
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.
LAZARUS
"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."
Packaged by Amanda Cavill
