The 49ers (1-2) are not making any excuses, though they say part of the problem is in the ambiguity of certain ''points of emphasis'' for NFL officials this year, rules already on the books that will draw more attention from officials.
''It does make you second-guess things,'' San Francisco linebacker Michael Wilhoite said. ''One thing I second-guessed was when the quarterback was running. Do I hit him or not? The hard part is knowing whether he's going down feet first or putting his head down and running.''
The 49ers were called for nine penalties for 107 yards in Sunday's 23-14 loss at the Arizona Cardinals. That was down from the 16 penalties for 118 yards called against San Francisco against the Chicago Bears.
''The frustrating part is not being able to get into a rhythm,'' Wilhoite said. ''Another penalty? Now what was called? You have to understand the rules and understand when you can hit a quarterback. I have to have the team's best interest at heart. At the same I want to play football and we all want to make the plays.''
The 49ers averaged fewer than seven penalties and 53 yards a game last season. The New England Patriots have been called for 30 penalties and an NFL-leading 322 yards and the Pittsburgh Steelers have been flagged 31 times.
The 49ers are on pace for 192 penalties and 1,626 yards. The Raiders drew 163 penalties and 1,328 yards in their record-breaking 2011 season.
''I feel the same way now as I did after the game,'' 49ers linebacker Dan Skuta said of an unnecessary roughness call that led to the Cardinals' go-ahead touchdown. ''I hit him with my shoulder, on his shoulder.''
Skuta tackled Cardinals quarterback Drew Stanton after he scrambled 7 yards up the middle on the disputed play.
''He was out of the pocket and if he's going to run like anyone else, I am going to hit him like anyone else,'' Skuta said.
''It's tough to guess when he goes down with his foot leading. I don't know what to do about that. I know you have to treat the quarterback differently. I think I understand that. I'm just trying to get him down.''
Also, All-Pro linebacker Patrick Willis was called for roughing the passer on the next play.
Willis was called for three penalties, only two were accepted, against Arizona.
San Francisco committed 103 penalties for 845 yards last year compared to 96 for 878 yards for its opponents. This year it's 36 for 305 as opposed to 25 for 166 for opponents.
''We can always play better,'' Skuta said. ''Talking about penalties is not going to get us any better. We can't worry about penalties. We have to get ready for the Eagles.''
The NFL has emphasized contact in the defensive backfield for this season.
The clipping penalty was also expanded to include contact by rolling up a player's leg. San Francisco tackle Jonathan Martin was called for a clip.
''I don't want to say too much,'' Martin said. ''It's just frustrating to see penalties at critical points of the game. It's just something I have to get better at.''
NOTES: The 49ers signed QB Josh Johnson to a one-year deal and waived TE Asante Cleveland. ... TE Vernon Davis said his ankle ''felt great. I feel like it's going to be a good week for me.'' Davis said he could tell on Saturday that the ankle wasn't right. ''It would have been a struggle. I wasn't quite ready.''
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