Plot hole: Apollo takes Adama down to the surface of Caprica aboard his Viper, yet the Viper is a single-seat fighter. This is the only time the single-seat craft is used to carry two people (though there is no shot of the two aboard - it is simply shown landed with the two characters nearby).
Plot hole: Starbuck and Apollo fool the Cylon basestar into believing they're two full viper squadrons. The Cylons haven't yet fully retreated behind Carillon (they order this as we watch), so their scanners should have been able to detect this deception far sooner than they did.
Plot hole: In order to extinguish an enormous fire aboard the Galactica, multiple explosives are placed on the exterior hull that are then detonated, opening the ship's interior to the vacuum of space and thus suffocating the flames instantly. No explanation is given for how everything is fine immediately after, yet everyone is up and around, breathing just fine. No holes to repair, etc.
Plot hole: After crashing on the planet, Starbuck's pants are shown torn open on his right thigh which is bleeding significantly. The child warriors find him and bandage his wound. When Boomer and Apollo arrive to pick up Starbuck, they give him a clean uniform. In the next scene, he is in that uniform, but his injured leg is wrapped in bloody bandages over the new pant leg. It seems unlikely he'd put the fresh pants on, then bandages. (00:44:40)
Plot hole: The borrowed (oh, all right, ripped off) plot of "The Guns of Navarone" does not translate well here. The premise, that the rag-tag fleet must pass through the "narrow corridor" guarded by the pulsar gun, is ludicrous. We're in outer space here. Outer space is very, very big. We can fly around one lousy little planet, no matter how many Cylons are "herding us" toward it.
Plot hole: The General informs the President that the Eastern Alliance has just launched its missiles. But the General has been sitting there throughout Apollo's speech with no communications device. So he couldn't have known that the missiles had been launched. (00:36:40)
Plot hole: This episode shows that, upon return from "long patrols", pilots are expected to use decontamination booths before rejoining the general population- a reasonable precaution. Strangely, Apollo and Starbuck walk among several ship personnel on their way to the two decontamination booths. If the pilots are walking among others on their way to the booths, this seems one rather pointless process. (00:21:50)
Plot hole: Galactica's sensors detect a second Battlestar, Pegasus- a shock to everyone aboard. Then its commander, Cain, speaks with Adama via video hookup, and announces that he'll be arriving at Galactica momentarily. Yet he arrives in a Galactica shuttle, marked "GAL 356", which hasn't been sent to go get him since they only just now discovered Pegasus exists. Even worse, this is the same shuttle destroyed several episodes ago when it crashed on Ice Planet Zero. (00:10:55)
Plot hole: Considering Galactica's mission of protecting the entire fleet, she wouldn't risk having recruits brought aboard that haven't been through a security screening already, especially a pair from a known warrior-like race, both of whom are wearing weapons openly. Nor would they be guarded by a crewman who willingly answers classified questions about locations of decorated Warriors posed by total strangers. Yet all of these gross security oversights occur in this one episode.
Plot hole: When Starbuck attempts to liberate Apollo, he captures two guards, saying "Now drop them or I'll incinerate you". They comply and he leads them to a room where Apollo's weapons and equipment are being analyzed. The analyst holds a radio on which we hear Starbuck say "Drop it or I'll incinerate you". First, Starbuck isn't transmitting. Second, he already has the guards disarmed and in custody. Third, the words are not the same as spoken earlier. Fourth, there's no reason such a transmission would have been delayed when sent radio-to-radio. (00:30:35)
Plot hole: The President and the General argue on a podium in front of a large gathering of citizens that are seated all around. When the General is told that their enemies have launched an all-out missile attack that will trigger their own automated response, wiping out both sides in the next six minutes, the audience is completely motionless and doesn't appear to react at all. They take the news that they are all going to die remarkably well. (00:40:25)
Plot hole: At about 35 minutes into the show, the fuel gauge of the shuttle shows 50 units of fuel remain. Five minutes of real time (and far longer in "story time") after, Starbuck begins counting down the fuel level, starting at 25 and dropping by 5 every 2 seconds. At that rate, the 50 original units should have run out within 20 seconds, and shouldn't have lasted over 5 minutes. 'Real world' use of fuel in space doesn't apply, as the canon of this show suggests fuel use is a constant to maintain motion, even in a straight line. (00:35:05 - 00:40:40)