"The decisions are quite hard to tell apart," Lavallee told the judge.
The Forest Service argued that the concerns over the separate tracts warrant separate complaints.
"There are differences that, when we get to the nitty-gritty, will matter," attorney Marissa Ann Piropato, representing the Forest Service, told the court.
She said combining the groups' concerns about the two tracts under the same lawsuit wouldn't necessarily be more efficient for the system.
The lawsuit was originally filed in U.S. District Court in Denver. A Colorado judge granted a Forest Service request to transfer the case to Wyoming in April.
Intervenors in the case on the side of the Forest Service include the state of Wyoming, Wyoming Mining Association, National Mining Association and BTU Western Resources.
Three other lawsuits WildEarth Guardians has filed against the BLM to contest Wyoming coal leases are pending before federal judges in Washington, D.C.