Chief Tyrol and Helo are told to put their hands behind their head by Pegasus marines. The camera cuts away to Boomer and back to Tyrol, who doesn't have his hands up any more, then to the marine announcing that Lt. Thorne is dead. In the next shot Tryol is shown lowering his hands.
During the end scene, Pegasus is flying in front of Galactica, but when both ships launch their alert vipers, they are seen across from each other with some distance in between.
At 42:18 Pegasus is flying in the fleet, ahead of and beneath Galactica. At 44:36 when Cain launches fighters, Pegasus is well separated from the fleet and turning toward Galactica. There was no scene that established this course change or separation from the fleet.
After the Battlestar Pegasus is identified and Commander Adama speaks with Admiral Caine, he orders the alert to be stepped down to "condition one". One might think that he would order "condition three", which is the lowest alert level. There is no reason why he should do this. As far as he knows, the cylons might have taken over the Pegasus. By keeping things on full alert, Adama is allowing for that possibility.
When Dr. Baltar and Number Six are escorted in to see the Pegasus' Cylon prisoner (21:33 in the broadcast version), the tape for Lt. Thorne's "mark" is visible on the floor as he stands guard.
Six is supposed to be an imaginary character in Baltar's head, but while inspecting the Cylon prisoner on the Pegasus you can see Six's reflection in the cell glass.
When the Pegasus raptor lands, Apollo gives the order to "dress and cover". While "dress" in this context means to fall in, forming perfectly straight and perfectly spaced lines, "cover" means to put on your cap, or your cover. Other than maintenance crews and marines, who already have their helmets on, no one has a cap.