In May 2007, Jenna Fischer fell down a flight of stairs and hurt her back. When filming for season 4 began, she had healed considerably, but was still not allowed to run. This is why Pam and Jim do not run the 5K.
Angela Kinsey (Angela) was pregnant during the filming of most of season 4, that's why the cameras never show her stomach.
Filming the run was not easy for the cast. On John Krasinski's YouTube series Some Good News (2020), he and Steve Carell commented on how the temperature that day was a sweltering 105 degrees.
The scene where Angela talks to Pam about her suspicion that Dwight killed her cat took a long time to shoot because Jenna Fischer and Angela Kinsey, who are good friends in real life, couldn't keep a straight face when talking to each other. It was so bad that they stopped shooting the scene and the director told them both to take a break while he filmed something else and they came back to it later in the day.
From this episode on, the closing credits will also play the intro music instead of no music.