SAN DIEGO — The missteps were both large and small, though in the end, all seemed equally debilitating for the Mets.

There was pitcher Noah Syndergaard and his ongoing battle to keep baserunners honest. There was third-base coach Tim Teufel and his rally-killing bit of hasty decision-making. And there was a feast-or-famine Mets offense that suddenly has looked feeble at the start of an 11-game West Coast swing.

By the end of a 2-0 loss to the Padres on Friday night in which the Mets managed only three hits, there was no shortage of places to lay blame.

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“When you’re hot, it looks easy, but it’s not,” manager Terry Collins said. “You know there are going to be times where you know you’re not going to hit the ball over the fence.”

The Mets (17-11) lost for the third time in four games, a streak that includes a pair of shutouts.

Syndergaard (2-2, 2.58 ERA) surrendered two runs and six hits in six innings, and his troubles with baserunners again came under scrutiny.

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Padres centerfielder Jon Jay, who has emerged as a pest for the Mets in the first two games of this series, played a role in both of his team’s runs. After a leadoff double in the first, Jay scored on Matt Kemp’s sacrifice fly. In the fifth, Jay’s run-scoring single to centerfield off Syndergaard drove in Jemile Weeks, who had stolen second to get into scoring position.

Padres lefthander Drew Pomeranz made the most of his support, holding the Mets to one hit in five innings. He struck out five. The Mets have scored only three runs against the four lefthanded starters they’ve faced this season.

With Pomeranz on the mound, Juan Lagares started in centerfield and Michael Conforto was relegated to the bench while nursing an 0-for-13 slump. Wilmer Flores started in place of second baseman Neil Walker, who was due for an off day.

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Rene Rivera started at catcher in an attempt to help control the running game with Syndergaard. Said Collins: “We’ll see if he can help out.”

Entering the game, 12 of 13 potential base-stealers had been successful against Syndergaard, an indication of his difficulties holding runners. But even with Rivera behind the plate, the Padres did enough to exploit Syndergaard.

Alexei Ramirez was the first to test the battery in the second inning, when he was thrown out at second base. It was the first time all season that a runner trying to swipe second against Syndergaard had been caught stealing. He was helped by Rivera’s strong throw.

But Ramirez swiped second easily in the fourth inning. And in the fifth, another stolen base proved to be key in a Padres rally.

Syndergaard walked the light-hitting Weeks to lead off the fifth. That sin was compounded when Weeks stole second, getting himself into scoring position on a close play. Jay followed with a single to centerfield.

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“It was good,” Rivera said of Syndergaard’s ability to deal with the running game. “He held the runners well. He gave me a chance to throw one guy out. The other one was close.”

Even Collins suggested that he saw improvement from Syndergaard. Still, it was clear that dealing with runners remains a work in progress.

While quickening Syndergaard’s times to the plate have been an emphasis for the Mets, a rival talent evaluator noted that the righthander has fallen into familiar patterns that made him vulnerable with runners on.

Perhaps more telling was Syndergaard’s issues with mechanics while working out of the stretch. He said he lacked sharp command of his fastball.

“I had pretty good command out of the windup with my fastball and my sinker,” said Syndergaard, who hopes to build off an adjustment he made in his final inning. “But in the stretch . . . I was trying to be a little too quick, my front side was flying open and everything was left in the middle part of the plate.”

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Of course, those faults might have been a side note had the Mets’ offense made good on its chances.

Some of it was bad luck, such as Matt Kemp’s running grab in the gap in right-center to rob Yoenis Cespedes of an extra-base hit.

But some of the struggles were self-induced, such as in the seventh inning, when Teufel’s ill-advised send of Asdrubal Cabrera effectively killed a rally.

With one out, Cabrera singled off reliever Ryan Buchter. Flores followed with a double that would have given the Mets runners on second and third with one out. Rivera was due up, but Collins had a bench stocked with potential pinch hitters.

Instead, Teufel waved Cabrera around. The Padres executed a clean relay, nabbing him at the plate. Catcher Derek Norris lost the ball after the tag, but the umpires upheld the ruling after Collins’ challenge.

Rivera popped up to strand Flores and end the Mets’ best shot of making some noise.

Fernando Rodney worked around a pair of ninth-inning walks to record the save.