Harper was booted in the fourth inning of the 5-1 loss Monday at Citi Field in Queens. The Mets had a 2-1 lead at the time.
Harper was at the plate at the start of the sequence. He stood in the batter's box and was struck out by Mets starter Steven Matz to lead off the fourth frame. Harper looked back at the home plate umpire as he was walking away from the plate following the strikeout pitch, which Carlson said painted the outside of the strike zone.
Rhys Hoskins hit a solo home run in the next at-bat before Matz walked Maikel Franco. Phil Gosselin lined out to center field during the next exchange, prompting Cesar Hernandez to step into the box with two outs. Matz tossed in a sinker for a ball before getting Hernandez to foul off another sinker.
He went sinker again with his third offering, getting in the 91.7 mph pitch for a called strike. Harper was barking at Carlson from the dugout during the exchange and the home plate umpire quickly made the motion that he was ejected from the game.
Phillies manager Gabe Kapler emerged to speak with Carlson, before Harper followed his lead. Harper got in Carlson's face to voice his displeasure before teammates and coaches had to restrain the superstar and escort him back into the dugout. Kapler managed to avoid an ejection.
"That can't happen," Harper told reporters, according to MLB.com. "I've got to stay in that game and be there for my team, the fans and this organization. I've got to be better."
"There was normal chirping from the dugout that is in every dugout every single night," Kapler added. "It was no different."
Hernandez ended up grounding a single to left field on the fifth pitch he saw from Matz. Roman Quinn entered the game for the Phillies, replacing Harper.
Aaron Altherr grounded out for the final out of the inning for Philadelphia.
Jeff McNeil hit a solo homer in the bottom of the fifth to push the Mets lead to 3-1. Pete Alonso was hit by a pitch with the bases loaded in the seventh to give the Mets a three-run advantage. Michael Conforto plated the Mets' final run with a sacrifice fly in the same frame.
Harper was 0-for-2 on the day with two strikeouts. He is now hitting .272 with five home runs and 14 RBIs in 81 games this season for the Phillies.
The Phillies and Mets face off in the second game of the National League East series at 7:10 p.m. Tuesday in Queens.