Near the end, when Kasidy hands Sisko a cargo box, she puts the handle down again. In subsequent shots, the handle changes between standing up and being down.
When Gul Dukat and Major Kira are discussing Tora Ziyal in the cave, Gul Dukat leans back against the cave wall. As he does so his Cardassian neck makeup tears and begins to come off.
When the Runabout is in the Badlands, stars can be seen through the window,
but the earlier exterior shot shows no stars were visible.