Quark's bruises and scratches get worse between shots, despite the fact that Dr. Bashir is in the process of healing them.
When Eddington is shot dead by the Jem'Hadar, a showed of sparks erupts from his body. Jem'Hadar weapons did not have this effect before or after this instance.
When first approached by Jem'Hadar fighters while aboard the runabout, Sisko says that they are "almost within firing range" while at a distance of .7 AUs. When the Jem'Hadar pick up their trail later on, they are said to be within .4 AUs and yet do not fire on the runabout for several minutes.
Kira and Odo appear to get along quite well, especially at 12:15 when they report on Morn's arrest while Dr. Bashir mends an assaulted Quark. They stand close and don't seem at all uncomfortable, even after their recent falling out in the previous episode Children of Time (1997). Yet not long after there is a plot explicitly about how they haven't been getting along, in Call to Arms (1997)--which takes place a month after "Children of Time," according to Kira. There Kira and Odo are noticeably cold toward one another and Kira explains to Dax that this has been a problem since she learned of Odo's romantic feelings.
Nog clocks the Klingons at 65 decibels, which he says is 5 decibels from disturbing the peace. 60-65 decibels is the volume of normal conversation. The Klingons are yelling at one another loud enough to be heard in a crowded bar. They must be at a higher volume than 65 decibels already.
Sisko fires into a seemingly empty room and shoots two Jem'Hadar soldiers who were "shrouded" (using a personal cloaking device). Shrouding has always shown to leave a distorted silhouette of the Jem'Hadar visible. No such effect is seen here prior to them being shot.
When Eddington and Sisko have concluded their back and forth in the Runabout, red blocking tape is visible (19:50 minutes) next to Sisko's chair.
After being confronted by Nog, Martok says something in untranslated Klingon to his men before they leave. As Nog is using a universal translator (and it is likely that the Klingons are as well), nothing that they say to him or in his presence should go untranslated.
Odd that Sisko believes the missiles will start a war. When he should clearly know the alpha quadrant is already at war with the Dominion. The Dominion had already tried to trigger a supernova to destroy DS9. Sounds like war is obviously already declared.
Nog is watching the Klingons cause a ruckus from a table in Quark's bar, waiting until they are loud enough to be officially disturbing the peace and he can arrest them. Either he is off duty, in which case it would not be appropriate for him to make the arrest, or he is sitting down on the job.
Eddington is hit square in the chest by a Jem'Hadar plasma rifle. Sisko insists they both get moving. Jem'Hadar weapons contain an anti-coagulant (to prevent wounds from healing) as well as a nerve agent. Having a great deal of experience fighting the Jem'Hadar, Sisko would be familiar with these aspects of their weapons. Eddington was a dead man walking the moment he was hit and Sisko would have known that.
Sisko declines the assistance of the Defiant in tracking down the Maquis base, saying it will drawn undue attention. As the runabout he is on has no cloak, it will drawn just as much attention as the Defiant, if not more so.
While in the runabout, Eddington accuses Sisko of spoiling their pleasant conversation about food by bringing up the Maquis attack against Cardassia. Eddington had just brought up the Dominion attack against the Maquis.
When Eddington cannot tell which of the figures in the fog is Sisko and which is the Jem'Hadar soldier, he waits until the Jem'Hadar emerges victorious in the struggle before shooting him dead with Sisko's phaser. He and Sisko both ignore the simpler solution; set the phaser to stun and shoot them both. Or, since Eddington already made public his intention to kill Sisko, he could have just shot both of them dead and been done with it.