Other mistake: In the CIC, Tigh challenges Apollo and asks why he isn't in the brig. Shortly after Apollo begins to explain the plan for the search and rescue of the Raptor downed on Kobol. He refers to it as "Raptor 3" when it is Raptor 1 they are looking for. Raptor 3 was destroyed when they first jumped to Kobol, Raptor 2 escaped back to Galactica, and 1 fell to Kobol. The Raptor on Kobol is referred to as Raptor 1 throughout the rest of the episode and on preceding episodes.
Other mistake: After she is sprung from prison and sneaks off the Galactica, President Roslin makes an appeal to the fleet to follow her ship to find the servant of the gods with the arrow of Apollo on Kobol. She is presumably speaking about Starbuck. But Starbuck was sent to and retrieved the arrow of Apollo from a museum on Caprica.
Other mistake: In the intro, when Tigh, Tory and Tyrol meet, Tigh is wearing Admiral's rank insignia of his uniform. His correct rank is Colonel.
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 ★