Continuity mistake: When Adama is trying to resign the President hands him a copy of the certificate she wants to present to him. The pen that was in the holder a few seconds ago has been removed to allow her to hand it to him without the pen in the way. (00:39:00)
Continuity mistake: In the scene where Apollo and Helo are boxing, Helo punches Apollo and this cause his head to bleed down his face. A few shots later the stream isn't as long.
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 ★