The new evidence came to light three months after the commission closed its public hearings in Greymouth.
Justice Young said the commission obviously decided it didn't need cross-examination to add to the inquiry.
"They would have been well aware of whether the evidence was conflicting (with previous evidence) or not."
Mr Grieve said the difference was this was new evidence coming from people who could speak with authority on them: "They needed to be cross-examined."
Justice Young said Mr Grieve should have tried harder at the time to have the hearings reopened.
"You may have lost your chance," he said.
Mr Grieve said the commission was set up to find the truth of what happened to cause the explosions at the West Coast mine in November 2010, in which 29 miners were killed.
Justice Young said he had the chance to file new evidence during the hearings but didn't.
Mr Grieve said while the applicants did not have new evidence, they should have been able to have the chance to question others who did have new evidence.
Whittall and Pike River Coal face a total of 21 charges, brought by the government's labour service related to failure of methane explosion management, strata management, ventilation management and mitigating the risk and impact of the explosion.
In July a Pike River Mine contractor Valley Longwall International (VLI) pleaded guilty at the Greymouth District Court to three health and safety charges.