The incidents in the videos in question all occurred before he and Jen were together, but that hasn't stopped her from being unhappy about them.
Jen "is very annoyed because it just means more attention on her and the kids as a result of Ben's actions," a source told E! News. "She tries to shield them from any and all publicity and scrutiny. She's taking her kids to school and to all of their activities. As far as they know nothing has changed and all is well. That is always her goal but she's been pretty frustrated with him."
Ben was forced to apologize publicly on Oct. 11 for an incident that occurred 14 years ago involving "One Tree Hill" star Hilarie Burton.
The actress claimed that Ben grabbed her breast in 2003 during an appearance on MTV's "Total Request Live." She tweeted that she "had to laugh back then so I wouldn't cry."
After video of the incident surfaced, Ben tweeted, "I acted inappropriately toward Ms. Burton and I sincerely apologize."
The incident resurfaced after Ben said that he was "sickened" by sexual harassment allegations against his old pal Harvey Weinstein.
Then, on Oct. 11, another video -- this one from 2004 -- surfaced of Ben being inappropriate with a female reporter.
In that video, he convinces the reporter to sit on his lap while he paws all over her. "They would like the show better if you did it topless, wouldn't they?" he asked her at one point. The reporter, though, has come out in Ben's defense.
"It has been blown out of proportion," Anne-Marie Losique said. "This was for the camera. You have to understand that we have done dozens and dozens of interviews like that. It was for a show I was producing, so I was not at all a victim. When the cameras rolled, we would start to do that game. As soon as it stopped rolling, there was none of that. He never touched me in any improper way. He was very respectful, I must say."