"It's not what you want, obviously," Girardi said. "You've got to deal with it. It's all over the game. That's what it is. As an organization, you try to prepare the best way you can by having depth. With some of the guys going down, we have guys coming back."
The Yankees placed Whitley on the 15-day disabled list on Friday, recalling right-hander Jose Ramirez from Triple-A Scranton/Wilkes-Barre. Whitley's place in the rotation will be taken by left-hander Chris Capuano, who will start on Sunday against the Royals.
Girardi said that he preferred not to risk having Capuano run the bases in an Interleague game after being sidelined all season with a strained right quadriceps. Nathan Eovaldi and Adam Warren are now listed as the probable starters for Tuesday and Wednesday against the Nationals in Washington.
Whitley said late Thursday that he had been feeling discomfort in his elbow for a couple of starts, but he never mentioned it to the training staff because he wanted to pitch and thought he could get through it. Girardi said that he wished Whitley had said something earlier.
"You want your guys to speak up, because maybe it could have been something that didn't get to this level," Girardi said. "It's hard to say because he wasn't examined the first time he felt it. He felt that he could get through it, he had never been injured before, never spent time in the training room.
"He was a guy that just went out and pitched. He said, 'I was still locating and still pitching well, so I didn't think much of it.'"
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch, on Facebook and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.