Voters are required to dip thir finger into a pot of ink after casting the ballots in order to prevent them from voting again at another polling station.
Al Jazeera has seen footage from three different polling stations across Kabul where voters were able to remove the ink, which is supposed to leave a stain for about two weeks, shortly after leaving the polling booth.
"We've spoken to the election complaints commission and the independent elections commission," Al Jazeera's Bays said.
"The election complaints commission chairman, the first he had heard of this was when I called him, but they say they have noted the problem and they will see if the can deal with it.
"I also spoke to some international election observers who are watching this and they believe that what might have happened is that they mixed the ink wrongly in this polling station."
With about 17 million people eligible to vote in 6,500 polling stations across the country it was unclear how widespread the apparent problem might be.
Shukria Barakzai, an Afghan MP, acknowledged that the allegations could be a huge problem for the presidential and provincial elections, but said it must first be clarified how many polling stations have been affected.
"From my understanding, and from my own pint of view, it maybe be just one or two or three specific centres where people may want to manipulate the process," she said.
"There are other ways in which people will be stopped from casting more than one vote, their card number must be registered.
"For sure there will be lots of shortcomings, but what is important for me and for the nation, we have to practice democracy."