In the beginning of the episode, while Fry and Bender are playing the board game, the color pattern swaps, with only the center of the board remaining unchanged.
During the trial, the Hyper-Chicken briefly is entirely blue.
When Zapp walks out of the old DOOP headquarters after being dishonorabaly discharged, while everyone looks at him, Kif's head is a different shade of green, looking more like an irradiated looking green.
DOOP is explicitly compared to the United Federation of Planets (even though Star Trek is considered taboo). Also, the "Neutral Zone" in which its headquarters are located may be a reference to the Neutral Zone between the Romulans and the Federation.