The (single) alien bad guy is Chavo, not Pancho...
Those looking for logic in the plot should generally eschew Lost In Space reruns, and this episode is no exception. It hearkens back to the silliness of the second season, and might be viewed negatively by many today for its stereotypical portrayal of Chavo. Perhaps that is why it is often skipped when the series is shown in syndication.
On the plus side, the episode's musical score is quite good, apart from the trite Mexican-style riffs. Those who want to hear Bill Mumy and Marta Kristin's rendition of Sloop John B. can find it in the multi disc Fantasy Worlds of Irwin Allen set from a few years back.