BrickLink was originally set up by a fan. Lego acquired it in 2019.
Cyber-professional Melanie Hoskin, a regular BrickLink user who has collected Lego for 45 years, said Lego did not believe a payment had been taken. She said the company at one point told her it would ban her from the site.
Lego has taken its online marketplace BrickLink offline after detecting what it described as unusual activity on the platform.
The site, widely known as the eBay of Lego, has been down for three days. The company has yet to disclose what caused the shutdown.
BrickLink is used by collectors worldwide to buy and sell second-hand sets, source individual bricks and purchase limited-edition releases.
On its homepage, the firm said that before restoring the service it wanted to"fully understand"what had happened.
"That means containing the issue, investigating how it happened and checking for related issues,"Lego said.
Lego published the update after being contacted by the BBC. A previous message had said the site was down for maintenance.
Earlier, a notice on BrickLink said the platform would be back online by Wednesday evening. That message has since been deleted, and no new timeframe has been given for its return.
It is unclear whether a payment problem reported by a user had any connection to the issue that took the website offline.