The Mets’ fragile rotation and battered bullpen has left manager Terry Collins open to criticism, even from his bosses, but Wednesday night’s meltdown against the Padres barely registered with team brass, according to sources.

Collins made several debatable moves, including the removal of starter Robert Gsellman after six innings in which he had pitched reasonably well, allowing three runs — throwing just 84 pitches — and later inserting Neil Ramirez into a bases-loaded jam created by Fernando Salas in the seventh.

Wil Myers blasted a game-tying two-run single (narrowly missing a grand slam) against Ramirez before Josh Smoker entered in the eighth and allowed the go-ahead homer to Hunter Renfroe.

Though Collins avoided an inquisition from general manager Sandy Alderson after the 6-5 loss, there are other recent moves by the manager that irked the GM, according to sources. Among them:

1. Before Tommy Milone’s first start with the Mets on May 10, the manager was told not to let the journeyman lefty work through the batting order a third time. But Milone was sent back to the mound for the sixth inning — after navigating a perfect fifth facing the top of the order — and surrendered two hits that led to a run, allowing the Giants to pull within 3-2. Jeurys Familia then blew the save in the ninth inning.

2. In Matt Harvey’s return from his three-game suspension for skipping a game, the struggling right-hander was sent back to the mound for the sixth inning in Milwaukee on May 12 to face the bottom of the order. To that point, Harvey had allowed two runs in a 2-2 game. But Harvey was hammered for three runs in the sixth, including two home runs. Alderson, according to a source, later gave Collins an earful for not letting Harvey leave the game on a positive note after five innings.

3. Collins continued to play Curtis Granderson this month instead of benching the veteran outfielder. Granderson, who entered Thursday with a .168/.236/.329 slash line, has shown improvement recently, but team brass, according to sources, wanted him benched on the Mets’ last road trip, when Collins had the option of playing T.J. Rivera in the outfield.

The fallout from the decision to let Harvey continue in Milwaukee may explain why Collins yanked Gsellman after six innings. The right-hander had allowed just three runs to that point and departed in position for the victory.

Only adding to Collins’ misery, he was informed from above before Wednesday’s loss, according to sources, that he should no longer divulge information about injured players to the media. The message irritated Collins, who traditionally has taken a straightforward approach in discussing injuries.

But a club source indicated there might have been a miscommunication that caused Collins to overreact. The manager convened with team officials, including COO Jeff Wilpon, on Thursday, according to a source, in an attempt to clarify the situation. When the subject was later broached during his pregame news conference, Collins indicated the objective is to avoid speculative timetables on when a player might return.

“I get in trouble because I try to be honest as I can with you guys and give you an honest look at things,” Collins said. “And then if it doesn’t happen, we look like an idiot, and we’re not, because there are no guarantees. We’re going to try to stay away from trying to predict anything except the fact there is a process involved of getting these injured players back on the field and it changes every day.”