The Electoral Reform Society has criticised the ballot papers used in the Scottish Parliament election.
Many voters said they had been confused by the system
But the group said the new single transferrable vote system used in the council elections was a success.
More than 100,000 ballot papers were spoiled, with many voters saying they were confused. There were also problems with the electronic counting system.
The Electoral Commission is carrying out a statutory review of the system to find out what went wrong.
Amy Rodger, Scotland director for the Electoral Reform Society, said it was too early to jump to conclusions over what had gone wrong.
But she added: "From what we have seen about the ballot papers that were filled in wrongly, it does seem to be something about the way it was designed or the instructions that were given.
"We need to look at this."
In contrast she said the council elections were an overwhelming success with very few spoiled ballots.
The society had previously warned against holding the council and parliamentary elections on the same day.
Meanwhile, an international observer of the Holyrood election claimed the problems were "totally unacceptable".
Robert Richie, executive director of US-based Fair Vote, said the difficulties amounted to Scotland's version of the "hanging chads" fiasco in Florida which marred the 2000 US presidential election.
"The most fundamental flaw was the ballot design of the party and constituency votes in two columns on the same page, rather than on separate pages," he said.
"Also, it seems confusion was caused by the change in the rules which allowed parties to use the names of leaders, rather than the party, in the first column.
"We saw this with the SNP's 'Alex Salmond for First Minister' and 'Tommy Sheridan Solidarity'. Some people may have thought they were voting for candidates."
The Scotland Office said it would launch an investigation "as a matter of urgency".