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

There was Noah Syndergaard and his continuing struggles 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. 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, even though his blazing fastball did not come with sharp command.

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. And in the fifth, Jay’s run-scoring single to centerfield drove in Jemile Weeks, who had stolen second to get into scoring position. Syndergaard’s troubles with baserunners came back to bite him.

Padres lefthander Drew Pomeranz made the most of his support, tossing five shutout innings and holding the Mets to one hit. He struck out five.

With the lefty 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.

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

Entering the game, 12 of 13 potential base-stealers had been successful against Syndergaard, an indication of his difficulties holding runners on base. But even with Rivera behind the plate, the Padres exploited Syndergaard’s weakness.

Alexei Ramirez stole second base easily in the fourth, and in the fifth, another steal proved to be key in a Padres rally.

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

Of course, Syndergaard’s 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 laced a single off reliever Ryan Buchter. Flores followed with a double that would have given the Mets runners on second and third with one out.

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.