When the group first lands on Tyree, Benjamin Sisko has a visible stain the front of his desert uniform. The stain is not visible in any subsequent scenes.
The energy released from the Orb of the Emissary travels from the planet Tyree to the Bajoran wormhole in a matter of moments. While the distance between the two points is not known, they are clearly in two different solar systems. An energy beam moving fast enough to bridge that distance so quickly would have to be traveling many times the speed of light, many times faster than the fastest warp-capable ship, and would be moving too fast to be visible.
The Rotarran is shown decloaking incredibly close to the star. A cloaked ship cannot raise its shields, and the ship could not have gotten as close to the star as they did with no shielding.
During the scene between Kira and Odo, around eighteen minutes in, there are two close-up shots of Nana Visitor's character in which her trademark Bajoran nose ridges are absent. The ridges are present in the wide shots.
In the final scene, Ezri Dax doesn't have dazzling blue eyes. They're more green/grey. Apparently, the actress wasn't wearing the colorizing contact lenses.
In the scenes on the planet Tyree, there are clearly hundreds of what are easily recognizable Joshua Trees, a highly distinctive, unusual-looking yucca "tree" found only in the Mojave Desert. If the producers had scouted a good shooting location for the "planet", such as these scenes filmed near Palmdale, California, the crew should have made sure there were not such iconic trees in any shot.
Around 9 seconds after Sisko closes the Orb box, a person with only their head visible can be seen moving behind a boulder behind Sisko at the right edge of the screen. The three other characters in the scene are in front of Sisko, so it is not one of them. Clearly a crew member who mistakenly moved into the shot.
When Quark shows up during the bloodletting ceremony onboard the Rotarran, Martok is as surprised as anyone to see him there. As commander of the vessel, Martok would have received any requests for someone who is not a member of his crew to board. Quark should not have made it that far into the ship, or onto the ship at all, without Martok's knowledge.
Ezri reminds Ben Sisko that he promised Jadzia that he'd "make things right." He made that promise to Jadzia's coffin, when he was alone, and the Dax symbiont was already on its way back to Trill. Ezri could not have known about that promise.
If "Benny Russell" is locked up for his own safety and can't be trusted with paper or a typewriter, why does he have access to a sharp writing instrument?
After declaring that she does not like raktajino, Ezri hands the beverage to Jake. She is closer to the replicator and could have just put the cup back to have its components re-processed.
The first time the Rotarran attempts to destabilize the star, Martok allows Worf to give the command to fire in order to honor Worf's commitment to Jadzia. The attack does not work. On their second, successful attempt, Martok gives the order to attack himself, thus negating Worf's purpose for being there.