Red Sox hitting coach Dave Magadan’s protests from the dugout led to his ejection.

AP / Dino Vournas

OAKLAND, Calif. — Major League Baseball, making good on its sudden interest in speeding up the pace of its games, made a quick example out of the Red Sox Friday night.

Home plate umpire Tim Tschida ejected Red Sox hitting coach Dave Magadan from the visitors’ dugout at McAfee Coliseum and the natural assumption, from afar, was that Magadan had been run for questioning Tschida’s ball-and-strike calls.

In reality, Magadan had seen fit to comment on Tschida’s refusal to allow outfielder J.D. Drew time to apply a pine tar-like substance to a new bat. Drew had broken his bat on a foul ball, and was quickly given a replacement by the bat boy.

But when Drew headed to the on-deck circle to apply some sticky substance from what players call “the Mota stick” — an encased tube that resembles a thick stick of lipstick, named after former major league outfielder Manny Mota, which features a substance that helps hitters grip the bat more securely — he was told that wasn’t allowed under baseball’s new rules, being enforced this weekend.

Magadan’s unfamiliarity with the rule and his subsequent reaction led to his ejection.

“We received memos 2 ½ weeks ago,” recalled Magadan yesterday, “with bullet points about things to improve the pace of the game, but I didn’t know [they had begun enforcing the new rules]. That’s my fault.”

Throughout the Red Sox clubhouse yesterday, there was surprise and resentment toward the new regulations.

“I don’t know if any of the staff had been told,” said third baseman Mike Lowell. “But I had no idea [they were implementing the changes]. I don’t see a pressing need to speed things up. Just let it be.”

Sean Casey, who, like Lowell, has played for more than a decade in the big leagues, couldn’t see the logic behind the incident.

“It doesn’t happen enough for it to become an issue,” he said, agitated. “It’s ridiculous.”

To ensure that no more players or coaches were caught off guard, the Sox held a closed-door meeting in the clubhouse late yesterday afternoon to go over the newly-announced regulations, something they should have done Friday, according to manager Terry Francona.

But pre-series scouting meetings and other issues got in the way Friday and Francona never had a chance to relay the information.

“That’s my fault,” said Francona.

The Sox fear that they may be targeted more than other clubs, in part because of their patient, grinding approach at the plate and their inclusion in nationally televised games, both of which add to the length of games. Before yesterday, according to research by the Elias Sports Bureau, the Sox were averaging 3:07 per game, 16 minutes longer than the 2008 MLB average of 2:51.

(To further illustrate the effect of a choosy lineup on time-of-game, the notoriously aggressive Los Angeles Angels of Anaheim were averaging game times of 2:46 before yesterday. The Yankees, meanwhile who take a similarly selective approach at the plate, were averaging 3:03, four minutes off the Sox’ pace.)

Lowell understands baseball’s interesting in speeding up games, but warns that it has to be done properly and not change the game’s natural flow.

“The way they want to go about it,” said Lowell, “players don’t care for.”

More than a few players noted the irony that Tschida’s ejection of Magadan and Francona’s visit with the umpire for a clarification took far longer than it would have taken Drew to apply the sticky substance to his bat.

Others wondered if the movement wasn’t an overreaction on baseball’s part.

“There’s no time limit in baseball,” said Magadan. “That’s part of its beauty. I know it sometimes frustrates some fans. But I like being at the ballpark.”

Moreover, as Magadan pointed out, part of his job responsibility is to make sure that Red Sox hitters don’t give away at-bats. By encouraging selectivity, which results in more pitches per at-bat, Magadan may be contributing to the length of games, but he’s also getting better results from his players.

“I don’t mind being out there another 10 minutes,” he said, “if it means we’re going to score more runs.”

Another contributing factor to the slower games for the Sox is the greater use of speed. With Jacoby Ellsbury, Julio Lugo and Coco Crisp all viable stolen base threats, opposing teams are throwing over to first base more often.

“You’ve got [opposing pitchers] holding the ball, stepping off [the rubber], throwing over … no question about it,” agreed Magadan.

Some hitters, too, were wondering if too much focus is being placed on hitters and not enough on pitchers who seldom observe the little-enforced mandate to deliver a pitch within 12 seconds of the batter being set.

“I don’t necessarily agree with this,” concluded Francona, “but everybody answers to somebody. You don’t want to lose sight of the fact that you’re trying to win games.”

smcadam@projo.com