When the defense force is returning to Earth, there are four fighters. After they get clearance to approach New Chicago, there are six ships. Obviously, this was a shot from an earlier episode.
In the opening credits of Flight of the War Witch, it is an extended version, with longer music and a few scenes from Season 2 Time of the Hawk, and only on the DVD release, not the blu ray version.
When Buck, Dr. Huer and Col. Deering first examine the probe in the desert, Col. Deering says the object has "no seam." But the probe prop is very visibly in two halves with a prominent seam, revealing the actors and the prop were almost certainly filmed separately.
A woman tells a man "You're black, you're beautiful", but the man was standing in the shadows, sporting a thick Mexican-style mustache. When he came out from the shadows, his skin was so pale, it could hardly be called "black".