The Swiss player was agitated by some of Nadal's challenges and completely lost his cool in the fourth set when a Nadal forehand that appeared to land beyond the baseline was shown to have clipped the line on the Centre Court screens.
"What can I say?" Federer said, when asked about the call at 0-2 30-30 in the fourth set that led to him being broken for a second time in the set.
"If I'm going to go against it, people will always say he doesn't agree whatsoever. I don't know how they developed this machine, if they took all possibilities into account: the way the ball travels, the way it bounces, 3D, the whole thing.
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"I told the umpire I was happy Nadal was going to challenge because I knew the ball was out. Then to see that it was in on a 30-all point, which was such a huge point, I was shocked."
The 25-year-old, who has raised doubts about Hawkeye in the past, was heard using an expletive during the changeover after saying the system "is killing me".
"I was frustrated because already I got broken and then to be broken this way was very irritating.
"The umpire told me, too, he saw the ball out. He couldn't believe it was in. I was like, all of a sudden, anything you challenge now is just going to go against me."
Nadal also criticised Hawkeye after his semi-final victory over Novak Djokovic. "I think the Hawkeye has mistakes sometimes," he said.
Wimbledon used the Hawkeye system for the first time this year on Centre Court and Court One, joining the Australian Open and U.S. Opens that have already employed it.
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