Over their last four games, three of them losses, the Mets have left 41 men on base. Forty-one. They rank in the top third of Major League teams in batting average, but the bottom third in actual run production. And that, for them, is a problem.

The trend manifested itself in various ways in their 5-3 loss to the Nationals on Tuesday at Nationals Park. The Mets’ woes were not due to stranded baserunners alone; Steven Matz allowed a season-high five runs in three innings, and a short bench provided manager Luis Rojas with little relief.

• Box score

But offensive issues nonetheless loomed large. A quick glance at three late-inning rallies reveals a combination of physical and mental lapses that plagued the Mets.

Top of the sixth: Tomás Nido grounds out

Win expectancy before the play: 22.1 percent
Win expectancy after the play: 16.1 percent
Net: -6.0 percent

Given the luxuries of a 30-man roster, the Mets assembled theirs so they could make their bench as potent as possible. Specifically, they carried three catchers so that they could pinch-hit or pinch-run for a backstop at opportune moments.

But when that exact situation unfolded in the sixth, Rojas stuck with Tomás Nido -- a career .191 hitter -- rather than turn to pinch-hitter Dominic Smith. Rojas indicated he was hesitant to hand the game-calling responsibilities midgame to rookie catcher Ali Sanchez, in what would have been his big league debut. And he couldn’t shift starting designated hitter Wilson Ramos to catcher because doing so would have forced the Mets to forfeit their DH. In addition, Jeff McNeil and Amed Rosario were both unavailable to pinch-hit due to injuries.

Given all that, Rojas stuck with Nido, who rolled over a chest-high breaking ball for an inning-ending groundout.

“Having Ramos in the DH spot, it kind of limits you to make that aggressive change in the sixth inning like that,” Rojas said. “It makes it a little bit of a tough decision there.”

Smith, who went unused in a similar spot last Thursday against the Red Sox, wound up striking out two innings later in what was, statistically, a slightly higher-leverage spot.

Top of the seventh: Pete Alonso strikes out

Win expectancy before the play: 34.5 percent
Win expectancy after the play: 25.8 percent
Net: -8.7 percent

Through 12 games, Pete Alonso is batting .174 with one home run. Even with an RBI single in the fifth inning on Tuesday, he is in a 2-for-22 funk with 10 strikeouts.

His issues are manifold. Although many around the Mets point to Alonso’s tendency to chase pitches outside the strike zone when he is slumping, he actually entered Tuesday’s game with a lower chase rate than he had during his historic rookie season. Of greater concern is the fact that Alonso is swinging and missing more often at balls in the zone, as he did on a 96-mph Tanner Rainey fastball with two men on base and no outs in the seventh.

Alonso has added a noticeable hitch to his swing this season, raising his hands a bit as he prepares to swing before lowering them as he launches into motion. According to SNY, he is currently working to quiet that movement, though he still featured it prominently in the loss on Tuesday night.

“It’s been tough stringing together the results, but they’re going to come,” Alonso said. “I know they are. I know what I’m capable of. I work hard. I work diligently and I’m a smart ballplayer. So this is rough now, but it’s temporary. Every ballplayer goes through struggles and rough patches during the season.”

Top of the eighth: Brian Dozier caught advancing

Win expectancy before the play: 15.2 percent
Win expectancy after the play: 8.0 percent
Net: -7.2 percent

Following a 67-minute rain delay, the Mets threatened again when Brian Dozier -- starting at second base with Robinson Canó and McNeil both nursing injuries -- singled to left. Two batters later, Dozier attempted to advance when Javy Guerra spiked a pitch in the dirt, but Yan Gomes threw him out. The play was close enough that the noticeably wet infield dirt could have made the difference between Dozier being safe and out.

“If you want to take a chance there, you’ve got to be 100 percent sure,” Rojas said. “We do want to create the pressure. That’s the way we want to work. That’s the way this game should be played. But obviously knowing the score, you’ve got the tying run at the plate is one of the things that you’ve got to keep in mind. … We’ve got to know how aggressive we can be. The scoreboard’s going to dictate that.”