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The 49ers won on Thursday night, but that doesn’t mean they were happy with the officiating.

Specifically, the 49ers want to know why the Seahawks weren’t called for pass interference, illegal contact or defensive holding — which the 49ers think they should have been. Coach Jim Harbaugh confirmed today that he has contacted the officiating department at the league office to ask about it.

“We’ll take that up with the officials and get their view of it,” Harbaugh said, via CSNBayArea.com. “I think it’s just important thing to address. What is this all being defined as? Is it physical play within the rules? That’s the biggest question. Is it within the rules what’s happening? We have to ask that question. We have to know what the interpretation is.”

San Francisco quarterback Alex Smith said he thinks Seahawks cornerbacks Richard Sherman and Brandon Browner should have been called for illegal contact “several times,” and that he noticed the Seahawks getting away with it in other games this season as well.

“If this is a point of emphasis of no contact after five yards, no question,” Smith said. “They’ve done it all year. When they played Green Bay, they were doing it to all those guys, [Greg] Jennings, all those guys. You turn on the Patriots [film] and same things. That’s what they do. It’s who they are. They’re good at it. It’s what they play, big corners, physical guys. I don’t know how we didn’t get a call. It seems like it gets called once a game and then it doesn’t get called again.”

Harbaugh also complained that Seahawks defensive lineman Chris Clemons should have been flagged for grabbing Smith’s facemask as Smith was trying to pass.

“It’s not impossible to throw the ball when your helmet is turned and you’re looking out the side of the earhole, but it makes it a lot harder,” Harbaugh said.

It’s probably safe to say these comments will be brought up when these teams meet again in nine weeks.