A company spokesman said: "An application was put in in January by the developer, not Matalan. "Matalan have no plans to go to the site in Cardiff."
Capital and Regional have not commented on the matter.
It's not known what effect this has on the overall project.
Retailer not going to be involved in stadium project
It's been revealed this week that Matalan will not take up 35,000 sq ft of space at the new stadium development. The company was named on the planning application but in a statement to BBC Wales, Matalan said the overall site developer, Capital and Regional, applied for the planning permission, rather than Matalan itself.