On the Defiant, Sisko's rank pips are misaligned. The third pip is higher than the second and fourth. Down on the planet, his pips are perfectly in a row.
It is established that Miranda's DNA is substantially similar to O'Brien's, as well as Rita Tannenbaum's. That analysis would be valid if Miranda were the daughter of the two, or at least granddaughter. But after 200 years and 7-8 generations down the line, it is more likely that each descendant - barring incest - has the genetic material of most of the original crew to more or less equal parts, not one dominant DNA in particular.
"Odo" is seen in the infirmary as a tub of translucent amber liquid. Odo's gelatinous form is usually more opaque and viscus. The material used for the prop does not match the usual CG color and quality of his gelatinous form.
When Worf is telling the Sons of Mogh that time is the colonists' enemy, the words do not match the movement of his lips. Given the high visible winds, it is likely the location dialogue had to be redubbed.
Dax and Worf are said to have married and had a family. Trill descendants and Klingon descendants are seen, but none that are both Trill and Klingon. If the only Klingon and the only Trill on the ship introduced their genes into the pool via their combined offspring, the only Klingons on the planet would also be Trill and vice versa.
Yedrin Dax's plan is allegedly to save Kira's life by creating a quantum duplicate of the Defiant and all inhabitant. The originals would be able to leave the planet and get Kira back to DS9 for medical treatment while the duplicates would crash back in time as had originally happened and create the colony. They'd still be killing Kira's duplicate, who would be a fully sentient being in her own right.
The descendants of the Defiant crew all bear a strong resemblance to their Starfleet progenitors. The O'Briens have red, curly hair, the Siskos have dark skin, etc. After 7-8 generations of breeding, it is not possible for such physical distinctions to persist, barring extreme incest. About the only ones that make sense are some of the Klingon descendants, whose facial ridges have faded over the centuries as they bred with the rest of the mostly-human population.
After the Defiant leaves orbit and clears the barrier, they scan the planet and find no trace of the settlement or its inhabitants. Before entering the barrier, they were unable to get readings from the planet's surface due to the barrier.
Given its proximity to Dominion space, it is unlikely that the colony would have been left unmolested by Jem'Hadar for 200 years.
Sisko tells Yedrin Dax that no one has the right to ask Kira to sacrifice herself to save 8000 others. However, we know that part of the psychological test given to perspective Captains involves ordering (not simply asking) a crew member to sacrifice their own life to save others.
Assuming Sisko has taken this test he would know that not only does he have the right to ask Kira to sacrifice her life, he is expected to order her to do so should the need arise.
The Sons of Mogh lament that they will not reach Suto'vo'qor because they will be wiped from history rather than dying in glorious combat. On a peaceful colony, there is little chance they would die in glorious combat anyway.
At 29:55, while Worf (Michael Dorn) is talking to the three Klingons, Parell (Marybeth Massett) says, " We've never plowed fields or milked chattel." In this context she is taking about milking cattle, not chattel. "Chattel" is defined as, "an item of tangible movable or immovable property except real estate and things (such as buildings) connected with real property," or "an enslaved person held as the legal property of another."
Yedrin's real plan, to ensure that the Defiant crashes back in time, is uncovered because Dax noticed flaws in the calculations that led her to realize the logs were faked. Yedrin used to be Jadzia. He'd know that she'd check for that.
Klingons refer to themselves as "son of..." their own fathers. In this context the Klingons would refer to themselves as "Sons of Worf" as they are descendants of Worf.