Wonder Yellow's weapon, the Peta Peta Hammer, is modelled after the Japanese-toy called the Piko-Piko Hammer. "Piko-piko" is the onomatopoeia for the chirping sound that the toy-hammers make when struck down on something. "Peta-peta" itself is an onomatopoeia for "stick" as in gluing something, "stroke" as in painting something, and "pressing repeatedly", which is the most likely one for the weapon.

The character Wonder Wonderland is a clear reference to the book Alice in Wonderland, her name is Allison Trump which is also the full name of Alice from the book.

In Operation 002-C, if you fail Wonder Pink's quick-time event near the end of the mission, Wonder Pink will pull out her phone and start having a sped up conversation. Failing this event 10 times in a row will actually play the conversation in normal speed and reveal that she is talking to Wonder-Cheerleader.

Wonder Pink: Oh my god! What's happening girl?
Wonder-Cheerleader: Nothing, girl.
Wonder Pink: How's Joe?
Wonder-Cheerleader: He's good, but he stood me up last night! Said something about the last movie in a red hot trilogy!
Wonder Pink: He did what? Tell him to quit going to the movies all the time. Such a deadbeat!
Wonder-Cheerleader: I know.
Wonder Pink: No, I do not think he is red hot... You are a crazy girl.

This conversation heavily implies that beyond physical similarities, Wonder-Cheerleader is actually Silvia from another Hideki Kamiya directed series Viewtiful Joe (both characters are voiced by Christina Pucelli), and that “Silvianne Lumiere“ is just an alias. This is also referencing the unmade third game in the intended Viewtiful Joe trilogy.