Plot hole: People who do not have their souls retrieved, before they are killed, will suffer the effects of the death on their soul, eg. the autopsied man has scars and cuts on his soul. So how come the woman who was crushed by a piano (whose soul was only ever retrieved afterwards) is unharmed in soul form?
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with the fleet after the emergency jump, Gaeta realizes a mistake has been made and says that Galactica's info is out of date.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.