Randy Knorr before a July game. (Alex Brandon/AP)

Ian Desmond was hit on the left shoulder with a 3-0 pitch from Marlins starter Henderson Alvarez after Bryce Harper hit a three-run home run in the bottom of the first inning. Home plate umpire Bill Welke immediately issued warnings to both dugouts. From the dugout, bench coach Randy Knorr appeared to yell at Welke, incensed by the warnings and that Henderson wasn’t ejected.

The Nationals took a 3-1 lead in the inning when Harper smashed his 20th home run of the season. Harper sprinted around the bases. It was his first home run of September and his first since Aug. 29, coincidentally also against Miami.

The next batter was Desmond. Alvarez fell behind 3-0 and then fired a 95 mile per hour pitch above Desmond’s waist that plunked him in the shoulder. Desmond took first base without causing any fuss. But the Nationals dugout didn’t appear too happy; at least Knorr didn’t. (“You don’t see too many pitchers 3-0 miss a spot like that,” center fielder Denard Span said.) From the top of the dugout step, he shouted and pointed at Welke and was then tossed.

“What the umpire did wrong, he obviously intentionally hit him, and to me, that’s an ejection,” Johnson said. “A warning doesn’t do anything. … But it’s real obvious when you give up a home run and then you get 3-0 on a guy and then you drill him. To me, you’re throwing at somebody on purpose. And I think the proper thing is to eject him. When you go on a warning, an errant pitch from one of our guys and I’m gone and the pitcher’s gone. But I just didn’t agree with the warning, and neither did Randy.”

Harper declined to address Desmond’s plunking after the game. At first glance, Desmond said he didn’t think he was hit intentionally.

“If it was, so what?” Desmond said. “If it wasn’t, so what? I’ll take my base. It helps my on-base percentage.”

Knorr, the Nationals bench coach, in the past has talked about how he doesn’t like warnings after players are hit by pitches. When he played, players were allowed to handle their displeasure with each other on the field. With a warning issued after the first batter is hit by a pitch the umpire feels is intentional, it becomes harder for the other pitchers to throw inside. And, the tension between the teams and any retaliation is prolonged to the next game.

“Let us do it and then bam, throw out the warning,” Knorr said in August. “You got us, we got you. Then it’s over. If the guy wants to charge, that’s his decision. [The umpires] think they’re protecting us, but they’re not. They’re prolonging it.”

Added Johnson after Thursday’s game: “I know they have instructions from MLB, anything that happens, warning. But it’s not like to prevent us from hitting anybody, not that we would. We’re trying to win a ballgame. But when somebody intentionally drills somebody, he should go. It’s that simple.”

After the warnings were issued, Nationals starter Gio Gonzalez spoke with Welke as did Johnson. Gonzalez believes that preemptive warnings in that situation makes it harder for him and other pitchers.

“I mentioned to the umpire, ‘I’m working inside. You can’t take that away from me,'” Gonzalez said. “He’s like, ‘I know. I understand. You pitch inside. Let’s make it very clear.’ He made it very clear where let’s get this game going.”

Desmond felt that the warnings changed the game some.

“If Gio accidentally hits somebody you lose your manager and your starting pitcher,” he said. “But, at the same time, if you’re pitching in the big leagues you should be able to throw the ball over the plate, pitch inside effectively, without hitting somebody. Obviously I understand that some balls get away, that’s kind of what I’m talking about — if there is an accident. That was pretty early in the game without much history there as far as I know to throw a warning out. But I can understand. They’re in a tough position. They’ve got to protect the players, they’ve got to protect themselves. Obviously you don’t ever want to see anything escalate where people get hurt

A day before, the Nationals and Braves benched were issued warnings after Anthony Rendon was hit by a pitch and after Atlanta starter Alex Wood exploded at home plate umpire CB Bucknor for strike calls. Bucknor tossed Wood and Braves Manager Fredi Gonzalez.

Johnson said he didn’t believe any tension between the teams would carry over to Friday’s game.

“I mean we’re still fighting for a playoff spot,” he said. “We’re not going to be throwing, I know some players that get a guy 3-0, it’s better just to drill ‘em. Send a message. I’ve seen it more here.”