Continuity mistake: The Galactica can retract her launch bay pods into the hull. She is shown doing it just before her first FTL jump. The instant before she jumps, the pods are suddenly shown in the extended position again.
Revealing mistake: After Dualla shoots herself, Gaeta hobbles back into the room. While the effects people made sure his real lower leg was erased from view behind his upper leg, they forgot to remove the shadow of the lower leg being cast upon the steel floor. The shot then changes away and returns to find the shadow has now been fixed the second time we see it.
Answer: The original BSG has something of a complex version history. Several versions exist, but the rationale behind what you're referring to is as follows. BSG, before anything else, was a TV series - the 'pilot episode' was a three-part tale called "Saga of a Star World". In that three-parter, a last-minute alteration to the script meant that Baltar was ultimately spared execution, because Glen A. Larson, the series producer, decided that he liked the Baltar character enough to keep him around for the rest of the series. The theatrical version, which was edited down from the three-parter and was shown in some countries before the US TV broadcast, lost quite a number of scenes, including the one where Baltar is spared. The real continuity of the series can only be found in the TV version - the movies, all of which were created by editing together existing episodes, miss out scenes leading to such apparent continuity errors.
Tailkinker ★