SANTA CLARA, Calif.– San Francisco 49ers coach Jim Harbaugh, a quarterback in his playing days, found himself playing defense Monday regarding the decision to play defensive end Ray McDonald against the Chicago Bears on Sunday.

McDonald was arrested last month on suspicion of domestic violence.

Harbaugh was reacting to comments made before Sunday’s game by California Lieutenant Governor Gavin Newsom, who insisted that McDonald should not be playing and labeled the situation a “painful affront to every victim of domestic violence.”

“Our response would be: We have two principles at play here,” Harbaugh said. “One is respect for due process. And we’re not going to flinch based on public speculation.”

McDonald has yet to be formally charged with a crime.

The 49ers, however, were guilty of making a bad first impression in their regular-season debut at Levi’s Stadium, where they blew a 17-0 lead and let the Bears leave with a 28-20 victory.

Aside from obvious mistakes committed by the offensive line, there was some controversy about the behavior of quarterback Colin Kaepernick. Or, more specifically, his language. Kaepernick insisted Sunday night he had no idea why he got flagged for using what was labeled by referee Carl Cheffers as inappropriate language following his first of two fourth-quarter interceptions.

Harbaugh said Monday he was still seeking an explanation, and he might have to go to the NFL offices to get one.

“I didn’t overhear that,” the coach said regarding comments Kaepernick might have made. “(The officials) didn’t come back and tell me.”

Kaepernick had a brief run-in with Bears defensive end Lamarr Houston after the play. Houston admitted afterward to saying “nice pass” to his rival. He insisted he didn’t hear Kaepernick’s response.

The penalty, normally a 15-yarder, only cost the 49ers 3 yards as it moved the ball half the distance to the goal from the 6-yard line. The Bears scored their go-ahead touchdown, putting them up 21-20, on the next play.

–The 49ers announced the signing of tight end Xavier Grimble and cornerback Leon McFadden to the practice squad Monday. To make room, the team waived cornerback Chance Casey and linebacker Shayne Skov, the latter notable because he was a star recruit for Harbaugh at Stanford whose pro prospects spiraled since he sustained a knee injury in 2011. The 49ers signed him as an undrafted rookie in May.

Grimble, 6-foot-5, 255 pounds, was originally signed as an undrafted free agent by the New York Giants on May 15 this year, then was waived Aug. 26. He was an All-Pac-12 selection for the last two years at USC, where his career stats included 69 catches, 731 yards and 11 touchdowns.

McFadden, 5-10, 190, was drafted out of San Diego State in 2012 by the Cleveland Browns in the third round.

He played in all 16 games as a rookie, including two starts, and had 19 tackles and one pass defensed. He was waived by the Browns last month.

NOTES: QB Colin Kaepernick fumbled once and was intercepted three times, giving him seven turnovers in his past nine quarters dating back to the fourth period of last year’s NFC Championship Game. Kaepernick led the 49ers with 66 rushing yards Sunday, 48 of which came on scrambles under duress from the Chicago defense. The Bears sacked him four times. … RB Frank Gore rushed for 63 yards on 13 carries in Sunday’s loss and scored on an 8-yard run in the second quarter. … TE Vernon Davis underwent an MRI exam on his left ankle Monday after he was bent awkwardly in the fourth quarter. … TE Vance McDonald sustained a knee injury in the first half of Sunday’s loss, but he played in the second half, but mostly as a blocker. … WR Brandon Lloyd was inactive. … RG Alex Boone made his first start after sitting out the entire training camp in a contract holdout and not getting on the field in the season opener at Dallas. … RT Anthony Davis (hamstring) missed his second consecutive game. Backup RT Jonathan Martin was beaten for sacks twice by Bears backup DE Willie Young.