When giant Mojo Jojo rips open the side of the building he's climbing with the Powerpuff Girls in tow, it shows the interior of the second floor of Cartoon Network studios with caricatures of the actual employees.
According to the Hollywood Reporter, the principal voice actresses Cathy Cavadini, Tara Strong and Elizabeth Daily went on strike because they felt they weren't being paid enough to do a movie, so Cartoon Network threatened to replace them with more popular voice actresses for the movie as well as for the TV series. Fortunately, a deal was made and Cavadini, Strong and Daily were able to reprise their respective roles as Blossom, Bubbles and Buttercup.
The plans for Mojo Jojo's "make the city a better place" machine have the serial number "PPG-801." Originally, the film was set to release on 8-01-02 (August 1st). Numerous other references to 801 appear in the film.
According to Craig McCracken, the executives gave him the freedom of creativity and went on to make it the way he wanted to. Then new executives arrived, who saw the completed film and said they should make it a colorful film; he calls this conflict in style as one of the reasons for the film to flop at the box-office.
When Mojo Jojo is reading the newspaper, on the back of it, there is an advertisement for the band "Gorillaz", the world's first virtual band. The title of the article states, "Gorillaz playing at Townsville Music Festival!" This was when Gorillaz released their first studio self-titled album back in 2001. This counts as the first time Gorillaz are featured in a Cartoon Network cartoon.
When the girls are watching the news reports about them, right after they walked off and just before the report on the Professor's arrest came on, the TV's show a news flash screen with cloud and thunderbolts. That is the same one used on the "News Flash" on older episodes of Sesame Street.
In the documentary The Powerpuff Girls: Who, What, Where, How, Why... Who Cares?, Craig McCracken expressed his disappointment with the movie, wishing he had made it brighter and sillier and not too heavy the whole time.