The four-time NL East champion Phillies were trying for their first 4-0 start since 1915.
"It's something that happens," Hamels said. "It's frustrating. You don't want to have games like this, especially to start the season."
Hamels (0-1) suffered through the second-worst start of his career, allowing six runs and seven hits in 2 2-3 innings. The lanky lefty's worst outing came during his rookie year. He allowed nine runs — five earned — in two innings against the Cubs on Aug. 24, 2006.
Hamels, the 2008 World Series MVP, arrived at spring training in excellent shape and was game-ready right from the start, even before Roy Halladay, Cliff Lee and Roy Oswalt. But the Big Three outdid Hamels the first time around.
"He'll be OK. It's his first game," manager Charlie Manuel said.
Hamels fell to 2-9 in 14 career starts against the Mets, who are off to a 3-1 start — all on the road.
"They just match up good," Manuel said. "They have good right-handed hitters."
Young became the first Mets pitcher with two hits in an inning and David Wright tied a career best with four hits.
San Francisco's Madison Bumgarner was the last pitcher to get two hits in an inning. He did it against the Cubs last Sept. 23.
"It's special to be a part of Mets history," said Young, who finished with three hits. "I never would've dreamed that."
Making his first start since joining New York, Young gave up one run and five hits, striking out seven in 5 1-3 innings. Young missed most of last season while recovering from shoulder surgery he had in August 2009. The 6-foot-10 right-hander was a solid pitcher with San Diego. He was 27-19 with a 3.44 ERA for the Padres from 2006-08.
Wright followed with a two-run single to left, making up for leaving two runners in scoring position in the first. After Carlos Beltran struck out, Wright stole second and a passed ball by catcher Carlos Ruiz allowed Pagan to score. Ike Davis and Brad Emaus added RBI singles. Young chased Hamels with a two-out RBI single that made it 6-0.
A fan wearing an orange hat ran onto the field and slid headfirst into second base during the middle of the ninth. Last year, a police officer used a stun gun to apprehend a fan who ran onto the field during a game at Citizens Bank Park.
Notes: Phillies GM Ruben Amaro Jr. said All-Star 2B Chase Utley "is not ready to run. That would be the next step, if he felt comfortable enough to do it. Hopefully we'll get him there at some point." Utley has been sidelined since the start of spring training with a right knee injury. ... Hamels was 0-4 with a 3.20 ERA against the Mets last year. The Phillies lost two of the games 1-0 and another one 3-0. ... A fan interfered with a foul ball hit by Philadelphia's Ben Francisco, leaning over the railing and knocking it away from RF Beltran in the fourth. Francisco was called out to end the inning. ... A crowd of 45,365 was the 140th consecutive sellout at Citizens Bank Park, including postseason games.