On Friday morning, Hill said Cherington sent an e-mail to the Marlins apologizing and explaining his organization's reasoning.
"We got an e-mail from their GM, saying they had some injuries, and they were working on some things," Hill said. "He apologized. It was during the game. I don't know if that meant he got a call from the league."
The Marlins didn't file any protest or issue any complaint over the roster that played to a 0-0 tie in a game shortened by rain with two outs in the top of the eighth inning. Actually, there isn't a process for a team to file a grievance, Hill said.
If MLB has an issue, a team could be disciplined and possibly fined.
"It's a Major League Baseball rule that you have to have a specific number of regulars," Hill said. "The league monitors all of our lineups. So if there was an issue, they will deal directly with the Red Sox."
The defending World Series champion Red Sox are an annual big draw when they travel from their Spring Training base in Fort Myers, Fla., to Jupiter.
Boston was considered a premiere game, and ticket prices were higher for Thursday than many other games at Roger Dean Stadium.
The Marlins heard from the league office a couple of years ago regarding a squad they sent up to face the Mets in Port St. Lucie.
Hill noted that on Thursday a majority of fans were for the Red Sox.
"It happens, but that's with them and the league," Hill said. "It's more of the Red Sox fans, who thought we were playing the Red Sox. They thought they'd get a lot bigger names than they got."
Hill downplayed the notion that there was any "outrage" in the Marlins' organization.
"That's a little strong," Hill said.