Floyd explains that the prefect’s nickname comes from how they jerked backwards when he and Jade approached them in the cafeteria.
It seems that he comes close to just naming the prefect “shrimp,” but then decides to go with little-shrimp-chan, given how small the prefect (apparently) is when compared to himself.
This is a rare example of the game assigning a physical attribute to the prefect–making them smaller than Floyd–but Floyd is the third-tallest student on the main cast (after Jack and Malleus) and, as Deuce explains, most students on campus are likely fairly small in comparison.
Twisted Wonderland Reference Note 