When the clerk in the station's assay office is entering in the items Vash is putting into her locker, the computer beeps after he enters in each item except for the last one. With the last item, the computer doesn't beep. The next beep is several seconds later after Vash says something and the Clerk says, "End inventory."
When Vash shows the Bajoran clerk the geode from the Gamma Quadrant, he says he's never seen anything quite like it; then he compares it with other things when adding it to the inventory.
O'Brien recognizes Vash, but based on her second TNG appearance nobody on the Enterprise knew she existed. In her second appearance, in Qpid (1991), O'Brien never appears and is not in the credits making it unlikely he would know her.
Quark offers Odo a latinum-plated bucket. It is revealed later in the series that latinum's normal state is liquid, requiring the gold to make it able to be handled.
When O'Brien is closing the hatch on the Ganges, a cord falls into view.
Sisko and others struggle to get a shuttle hatch open before the occupants run out of oxygen, but they could have simply transported them out.