|Getty Images Image caption Ed Sheeran said he wanted to stop his fans being ripped off by overinflated ticket prices
The Shape of You singer imposed strict rules for entry at his 18 gigs to try to stop the reselling website Viagogo selling overpriced tickets.
Tour promoter Kilimanjaro Live said thousands of fans with invalid tickets from the website were offered new ones at face value.
Viagogo has been asked to comment.
Sheeran had said he wanted to stop fans being ripped off by secondary ticket sites, many of which are believed to be used by touts selling at overinflated prices.
Ed Sheeran praised for thanking police
Ed Sheeran stops gig for the loo - twice
How Ed Sheeran is tackling ticket touts
The majority of ticket resellers had agreed not to list tickets for the stadium tour but Viagogo did not follow suit - and fans who bought tickets from the company were told they were cancelled.
They were given a letter after arriving at the concert to prove they were invalid - which is needed to gain a refund from the reselling site - and then offered new tickets at face value for that night's concert.
|Principality Stadium Image caption Ed Sheeran was the first artist to play four successive nights at the Principality Stadium
"We ended up dealing with just under 2,000 fans in Cardiff," he said.
"Unfortunately they included people who had paid several thousands of pounds for tickets."
Claire Turnham of Victim of Viagogo, which was based at the box office at each of the tour's venues to advise those affected, said staff had been "extraordinarily busy".
"The amount of people who have been affected... it's a staggering number," she told BBC Radio Wales' Good Morning Wales.
"It's all about people power, this is about people joining together, fighting back."
|Getty Images Image caption Glastonbury operates a similar ticketing system to the one used on Sheeran's tour
His ticketing system is not a first - Glastonbury and the West End musical Hamilton operate similar policies - but no-one had attempted it for a large-scale tour before.
Viagogo is currently facing legal action over alleged failure to comply with consumer protection laws.
On its website it protests against concert promoters who deny entry to fans using resold tickets.
"These types of entry restrictions are highly unfair and in our view, unenforceable and illegal," it says.