Visible crew/equipment: During the escape with the Eidelons, when Aeryn's holding the baby and says, "There's too many boot prints and they're fresh. We're not alone," a moment later there's an explosion, then after she shouts, "Inside," and leaves, in the next wide shot the springboard can be seen propelling an Eidelon stuntman. Plus the fact that in this shot Aeryn is still by the wall.
Visible crew/equipment: While Moya is under attack by the Tregans, after D'Argo asks Pilot if Moya can free herself from the hauling lines, when Pilot shouts, "The Tregan ship is pulling us in," we can see the puppeteer rods under Pilot's arms and also the fingers of one of Pilot's puppeteers.
Revealing mistake: When John uses Scorpius as a shield and takes cover in front of him, as John fires at the Tregans behind Scorpius, there are round black devices attached to the back of Scorpius' suit that are there for the gunfire special effects, which suddenly appear then disappear after.
Continuity mistake: When Crichton talks to Harvey (Scorpius in his head) about the Wormhole Weapon engineering project, one of the women in the scene leans on the hood of the car, with her glasses in her hand, chewing on the left arm of the glasses (the right arm is folded). The camera angle changes, and the arms are switched. The camera angle changes back, and the arms are switched back.