At approx. minute 62, the six survivors walk across the rim of a small mountain. The Doc is still in the picture even though he died couple minutes earlier. In the next scene he is gone and there are only five people left. The two scenes are even blended so at some point you can see six and five people in one shot.
Both Sky Marshal Phid and Anoke wear the incorrect epaulets. The epaulets they are wearing are of the Rank of Lieutenant not Sky Marshal. Zander Barcalow, a Lieutenant in the first film, wears the same epaulets.
When the Marauder team is stripping down in preparation for the BioScans, Lt. Link Manion removes her shirt twice.
While Beck, Rico and Dix are talking in the bar, Capt. Beck removes her garrison cap. Thoughout the rest of the scene the hat reappears on top of her head and then disappears when camera angles change. This is at the 13:00 minute mark of the film.
When the Geronimo is knocked out of warp it is shown suddenly returning to normal speeds, but the windows behind Lola still show space speeding past at warp speeds.
From 21:12 to 21:18, on the far left side of the frame, the knees of a kneeling soldier on a barracks roof instantly materialize over the wall. As the scene pans up, the knees eventually end up in a proper placement. Furthermore, the actor shakes the rifle as if firing, but no muzzle-flash nor audio accompany the action.
Near the end, Lola hits Sky Marshall Anoke first on the back and then in the face. The face-punch never touches his face.
During the scene when the Federation troopers walk through the desert, a slow pan of a shot of a bug dead and half buried in the sand will reflect a tint from the camera above.
Slightly less than 2 minutes before the closing credits appear, during the ceremony in which Sky Marshal Anoke is being commemorated, a sign is shown that says "Do your part and buy the Sky Marshal Anoke commemorative compilation." But "compilation" is misspelled as "complilation" with an L before the first I.
At around 12 mins into the film, a female trooper interrupts Sky Marshal Anoke to ask for an autograph for her brother. He inquires what his name is, and you hear 'Kevin' off screen. This voice is clearly not of the actress who asked for the autograph, and was added in post production.
At 25:28 into the movie, when they pan through the main control room, when the light flickers you can see the reflection of the camera man and the crew standing behind him.
When one of the exploding pill bugs pops open, you can see a cable half-buried in the dirt leading away from it to the right side of the screen.
Rico is repeatedly referred to as the "Hero of Planet P", the man who captured the Brain Bug, but that was Sergeant Zim in both the book and the first film.