When Sisko is talking to Jake in their quarters regarding Jake's date, Jake is first seen leaning over the arm of the chair, with his head propped up on his hands. A moment later, he is sitting up, facing a slightly different direction. Shortly after, he is again in his original position, and finally, when his father crosses the room, he is sitting up once more.
At 4:00 Major Kira (Nana Visitor) is performing a spiritual exercise in her quarters, and on her right shoulder a polio vaccine scar is clearly visible. Not something someone in the 24th century from another planet would likely have.
When escaping from the Cardassian guards, some of the Bajoran prisoners stay behind to hold off the attackers. There is no reason the runabout couldn't have beamed the last few Bajorans out rather than leaving them behind to die.