Continuity mistake: In the last battle scene in the miniseries, above Ragnar, all the civilian ships Jump away and Commander Adama orders all the vipers to land inside Galactica's landing bay. At one point, Dualla reports that two vipers are still out in the fight - Starbuck and Apollo. When Starbuck pushes her viper and Apollo's towards the landing bay, there's a shot of one of the basestars firing a missile, which hits Galactica. In this scene, we can see (and hear) 3 vipers, one of which is firing at a Cylon raider in the distance. They couldn't be Starbuck or Apollo, since Starbuck's viper and Apollo's were joined together and the mystery vipers are not, nor are they any of the other pilots, since only Starbuck and Apollo's vipers were still out, as Dualla has stated.
Continuity mistake: When Chief Tyrol finds Jammer, Socinus and Cally at the still, they are standing in that order with Socinus behind and between the other two. The shot cuts to the chief dumping out the booze. Then it cuts back to the trio. Now their positions have changed. Now Socinus is on the left, Jammer on the right with Cally behind and between the guys. (00:08:20)
Factual error: Early in the episode a damaged Viper makes its way back to Galactica with its port-side gun trailing smoke as if in an atmosphere. But in a vacuum, the smoke wouldn't trail. It would build upon itself much the way shaving foam does when slowly leaking from a damaged can, unless the ship changed course and/or speed and then the smoke would appear to do the opposite - ship turns right, smoke moves off to the left because it remains on its original course regardless of what the ship does. The gun is not propelling the smoke rearward. The ammo inside is simply burning. (00:05:15)
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.
Continuity mistake: Season 1 Episode 13 "Kobol's Last Gleaming Pt 2" Apollo leads a strike force to capture Colonial One and arrest President Roslin. We see his vipers and raptors approaching Colonial One, all alone a little way from the fleet. A few scenes later, (before Apollo's force reaches it) Boomer launches in a raptor and as it leaves the bay, we see Colonial One in it's normal position off Galactica's port bow.
Continuity mistake: Episode 2-13, 'Epiphanies': When Baltar is led by the wrist along a corridor by Number Six, two crewmen pass Baltar on his left, headed the other way. The shot from behind Baltar places the crewmen immediately to Baltar's left when the shot is cut to a shot looking in the opposite direction as Baltar approaches the camera and the crewmen are now far behind Baltar, instantly. He is speaking continuously before and after this shot change, so there is no 'time passage' between the shots.
Plot hole: Gaeta and Tigh both reference the fact that the Galactica crew computes the changes in stellar drift for FTL jumps and then sends out the info to the rest of the fleet for their use. However, when they fail to rendezvous with the fleet after the emergency jump, Gaeta realizes a mistake has been made and says that Galactica's info is out of date. This creates a major plot hole because if Galactica sends out the new info to the fleet, Galactica would always have the most up to date info for FTL jumps. The crew would be able to solve the lost fleet crisis by simply reloading the last coordinates that Galactica sent out and jumping there where the fleet would be waiting for them. There would be no need to go back to the previous coordinates and recompute the jump.