Beatrice Wankmeister's hair is shorter than in the hologram which Roger's son showed him in the end of the previous game Space Quest IV: Roger Wilco and the Time Rippers (1991). This can be explained by that the hologram was made in Beatrice's later years.
On the planet Klorox II, when Roger enters the building - a pukoid's head can be seen at the bottom right corner of the screen, watching Roger and then gradually disappearing from view. When Roger approaches the computer, the pukoid charges him from the left side, before the head fully disappears from the screen corner - although it is clearly the same creature.
The female Terminator WD-40 claims that Roger did not pay for the whistle which he had obtained in the second game Space Quest, Chapter Two: Vohaul's Revenge (1987). However, in the order form which Roger mailed to receive the whistle it was written "Free Labion Terror Beast Mating Whistle".