Bryce Harper and umpire Marvin Hudson get into a shouting match at home plate, a confrontation that led to Harper’s ejection. (Jonathan Newton / The Washington Post)

For the second time in a week, Bryce Harper and Manager Matt Williams were ejected from a game for an exchange with an umpire. But this time, in the third inning of Wednesday night’s game against the Yankees, both were dumbfounded over the reasons home plate umpire Marvin Hudson did.

“I can’t explain it,” Williams said. “I don’t believe there’s anything that warrants throwing him out of the game right there.”

“I don’t think 40,000 people came to watch him ump tonight,” added Harper, after his fifth career ejection. “Plain and simple. Especially when we’re playing the Yankees. The Yankees are a good team, we’re a good team and we’re rolling. I don’t want to get tossed. There’s no reason for me to get tossed in that situation. I don’t think I did anything bad to get tossed. Maybe he just had a bad morning or he didn’t get his coffee.”

The dispute started in the bottom of the third inning when Yankees starter Adam Warren threw Bryce Harper a slider that Harper believed to be low, and the Nationals right fielder stepped out of the box after the unexpected strike call from Hudson. According to MLB.com’s Gameday strike zone, the pitch was indeed low. Harper shook his head and said something about the called strike while keeping his left foot in the batter’s box. With the new pace of play rules, players get letters in the mail from the league about staying in the batter’s box in between pitches.

“I just looked off and put my head over,” Harper said. “I looked at the floor and was like, ‘That was a little down, don’t you think?’ He told me to get in the box and I was already in the box. Then I was standing there looking at the pitcher.”

This is when the real dilemma began. From the dugout, Williams voiced his disagreement with the pitch to Hudson, who took off his mask to talk back. So Harper stepped out of the batter’s box.

“I didn’t need to be in the box while he was chirping at Matt,” Harper said. “Then they were going at it. He told me to get my butt in the box. I was like ‘Well, you’re still chirping at my manager so let me take a minute.’ He told me to put my foot in the box and I said I’ll take the fine. It’s not a priority for us to get in the box unless we really need to. I was just taking my time. Once I put my foot back in the box, I says ‘This is where I was.’ He rung me.”

Harper, in fact, pointed at the spot in the dirt where his foot left a mark. From the on-deck circle, Ryan Zimmerman threw up his hands in disbelief at the ejection.

“At the point in which [Hudson] took his mask off, Harp was back in the box, ready to see the next pitch,” Williams said. “And I just don’t feel it was warranted so that’s why I went out and argued it.”

After the game, Hudson offered an odd explanation. He insisted that Harper was not ejected because of the batter’s box issue. “Had nothing to do with the box,” Hudson said. That fits MLB rules, which state a batter’s box violation is an umpire warning on first offense and league penalty on the second offense; not an ejection.

The reason for the ejection, Hudson said, was something else.

“He didn’t like the pitch and I let him have his say going and coming,” Hudson said. “The dugout didn’t like it, and one thing led to another and I had to run him. I had to eject him.” Hudson added Harper also said something to him as he got in the batter’s box.

After the ejection, Harper yelled in Hudson’s face and Williams came out of the dugout to argue. Williams pushed Harper away and third base coach Bobby Henley stepped in to nudge Harper off the field. Williams yelled at Hudson, too, and was soon ejected. Before he left the field, Williams kicked dirt on home plate. After the game, he was visibly frustrated with the situation as he spoke with reporters.

“Doggone it, he’s our best player and arguably the best player on the planet right now,” Williams said. “And we need him in the game. And I don’t feel as if there was any need to throw him out. So that’s why I went out and argued.”

Harper said Hudson appeared more angry at Williams than him. Williams said he told Hudson from the dugout that the called strike was too low.

“I let him know I felt it was low and he was talking to me,” Williams said. “He wasn’t talking to Bryce. He was talking to me. And then the next thing I know, Bryce is thrown out of the contest.”

Said Hudson about Williams: “He said something he shouldn’t have.”

After the game, Nationals officials lodged a complaint about Hudson with MLB. Some team officials were steamed about the ejection because they believe Hudson purposefully seeks out confrontation. “He baits players,” one official said.

Hudson and Harper have disagreed before. In 2013, Harper hollered at Hudson after Hudson said Harper did not check his swing in the ninth inning of a game against the Braves. In 2012, Hudson even ejected then-Manager Davey Johnson, who has been tossed only twice this decade. Harper said he didn’t even remember the first incident with Hudson.

After Harper was ejected by Rob Drake last week, he said he didn’t “like getting talked down to by an umpire.” Asked if he felt umpires held him to a different standard than others, Harper said he didn’t know.

“I really have no idea,” he said. “I want to stay in the game. That’s the biggest thing. I made sure I didn’t look at him or anything like that. That was the biggest thing. If you don’t look at him and you’re looking down, you’re not showing the guy up. Once you tell me to get in the box then I’m gonna take my time. I mean truly, I don’t need to get in the box when you’re chirping at my manager. And I don’t need to be in the box with your mask off. I mean that’s an equipment violation if you have your mask off. So nothing I can do.”

Harper was replaced by Michael A. Taylor, who was called out on strikes by Hudson. Zimmerman was called out of strikes, too, to start the next inning, on a called third strike that appeared a tad inside in MLB.com’s Gameday strike zone. The Nationals eventually came back to win the game and Alex Rodriguez, too, wasn’t happy with the strike zone. Harper and Williams watched from the clubhouse.

“Thankfully we won a 3-2 ballgame,” Harper said. “Drew Storen came in and closed the door. Got my lift in early. That was good. Of course, I want to be on the field. I don’t need to be in here watching the game on TV. I need to be on the field and helping my team win and in those situations I want to stay in the game … especially in the third inning. I mean that’s a joke getting tossed in the third.”

Barry Svrluga contributed