He was especially upset that plate umpire Sam Holbrook ruled Juan Lagares was hit by a two-strike pitch while trying to bunt, which sparked the Mets' four-run ninth-inning rally.
"I'm not supposed to complain about calls, but the league needs to look at it," Mattingly said. "I don't understand a lot of it tonight. I understand the Marlins are not supposed to be good this year; I guess it's OK to pile on.
"It's got to be better than that."
Holbrook said Lagares didn't offer at the pitch, and the ruling was upheld by a replay review.
"That was a shaky call," Mattingly said. "Sam said he was trying to get out of the way. But he never pulled the bat back in any way, shape or form."
Said Mets manager Mickey Callaway: "I saw a guy trying to get out of the way of a fastball that was going to hit him in the face."
Mattingly also complained that Holbrook missed two pitches by the Marlins that should have been strike three, calls that led to a Mets run.
Mattingly's postgame feelings might have been different had the Marlins converted a great opportunity in the ninth inning. Miami loaded the bases with none out against closer Edwin Diaz, who then struck out the next three batters to end the game.
The Associated Press contributed to this report.