The Pittsburgh Pirates failed to score with the bases loaded in the ninth inning for the second consecutive game against the Colorado Rockies, though this one came with controversy.

The game ended abruptly when baserunner Billy Cook was called for interfering with third baseman Kyle Karros, who fielded Jake Mangum’s ground ball for what appeared to be game-tying infield single.

Instead, Karros complained and the umpire crew gathered and signaled an out to end the game. Pirates manager Don Kelly ran onto the field to argue the call but to no avail. It was a wild ending as the Rockies won another one-run decision, 2-1, Saturday night at Coors Field.

“They said that they got together and that Billy kicked his glove — which he did, looking at the replay,” Kelly said on the SportsNet Pittsburgh postgame show. “I just didn’t know if you saw that why it wasn’t called immediately, why you had to get together to call it.”

The Rockies (30-47), who own the worst record in baseball, beat the Pirates, 4-3, on Friday night and can clinch a three-game sweep Sunday in the series finale.

Brandon Lowe led off the ninth with a double to right-center off Brennan Bernardino and reached third when Bryan Reynolds hit a sharp single up the middle that Castro made a diving stop to save a run. After Bernardino struck out Ryan O’Hearn, the Rockies replaced him with Jaden Hill, who hit Nick Gonzales with a pitch to load the bases.

Hill responded by striking out Tyler Callihan, who went down swinging with the bases loaded in the ninth inning for the second consecutive game. When Mangum hit a grounder to third, Cook was called out for interference for running in front of Karros.

Cook was stunned by the call, though he admitted that video review showed his cleat made contact with Karros’ glove. With two outs and the bases loaded, he was running on contact. Upon reflection, he wondered whether he could have caused a rundown to allow the run to score.

Cook called the result “unfortunate.”

“I know that I can’t get hit by the ball, so I beat the ball,” Cook said. “No contact with the third baseman. I’m just running, and I guess he clipped my cleat just barely because I was past him. I was surprised that they didn’t call anything then, all of a sudden, they did.”

It marked the seventh consecutive loss with reigning National League Cy Young Award winner Paul Skenes on the mound. Skenes (6-7) took the loss despite delivering his second consecutive quality start, which was marred by familiar faults from the Pirates: defensive mishaps and a lack of run support.

“I thought he pitched well,” Kelly said. “I don’t know if he necessarily had his best stuff. But the way that he competes is unbelievable. He found a way to get through six innings and gave us a chance to win.”

Jake McCarthy took advantage of shaky defense to hit an inside-the-park home run in the first inning and scored from second on a single in the third to provide both runs for the Rockies.

Skenes recorded eight strikeouts and allowed two runs on four hits, two walks and a hit batsman in six innings. He threw 63 of his 104 pitches for strikes, drawing 19 whiffs and 10 called strikes.

The Pirates gave Skenes an early cushion when Spencer Horwitz took advantage of a miscue between Rockies shortstop Ezequiel Tovar and third baseman Willi Castro on a first-pitch foul ball. Horwitz hit a 2-1 fastball 434 feet to right field for his fourth leadoff home run and a 1-0 Pirates lead.

The Rockies responded with a leadoff spark of their own, as McCarthy raced around the bases after Mangum missed a diving attempt at a line drive and Callihan booted the ball at the wall. Of the 30 career home runs allowed by Skenes, nine came in the first inning, with seven by leadoff batters.

“Off the bat, I had a great jump, great route. Everything up to the catch I felt like I did exactly everything I needed to do. As an outfielder, once you do those things, it’s about making the final catch,” Mangum said. “Unfortunately, I watched the video and it was about two inches away from my glove. … If we make the catch, we’re celebrating instead of being upset.”

Mangum made another mistake in the top of the second, when he doubled to right field but was thrown out when trying to advance to third on Jared Triolo’s grounder to short.

Colorado had the same problem when Cole Carrigg started the second with a leadoff double down the right field line but was picked off when Skenes turned to throw to second baseman Brandon Lowe, who fired it to Gonzales at third.

But McCarthy had a hustle double in the third on a sharp grounder to right-center, then scored on a single to left by TJ Rumfield to give Colorado a 2-1 lead.

Where Rockies starter Tomoyuki Sugano retired a dozen consecutive Pirates hitters, Skenes got out of a jam in the fourth. After Troy Johnston drew a leadoff walk and Carrigg was hit by a pitch, Skenes got Edouard Julien to line out to center and Tovar to ground into a double play.

It wasn’t until the fifth that Skenes was able to retire the first two batters of an inning, as he sandwiched strikeouts of Sterlin Thompson and Castro on changeups around a McCarthy groundout to second.

“It was a grind,” Skenes said. “I had to really reach in and figure out how to execute some pitches because it wasn’t very good. … I’m glad it wasn’t worse.”

Sugano held the Pirates to one run on four hits without a walk while recording five strikeouts in six innings. They finally reached base when Callihan drew a walk against reliever Jimmy Herget in the seventh, only for Mangum to ground into an inning-ending double play.

But the Pirates had a chance to win in the ninth and came up short again when Cook was called for interference and the game ended in abrupt fashion.

“It’s a tough loss,” Kelly said. “Two in a row, to have guys in scoring position late in the game. … With the rally in the ninth, we have to find a way. We have to score there.”