At the start of the courtroom scene with Dax on the stand, Sisko has four pips on his uniform. (Four represent the rank of Captain.) Partway through the scene a pip is missing; only three are visible throughout the scene without any visual evidence of being removed. In the next scene all four are restored.
When looking over the list of casualties from the "civilian" ship, Ch'Pok and Sisko identify the passengers as, "merchants, soldiers, artists, shopkeepers. Children." Earlier, Odo and Sisko had determined that there was no one aboard that ship who'd hold a grudge against the Federation or would have any desire to engage the Defiant in combat. Soldiers of the empire would surely view a Starfleet vessel as an enemy.
In order to have an extradition hearing, the Federation must first have a reciprocal extradition agreement, which would allow an extradition. The Federation has never had such an agreement with the Klingon Empire, because the Klingons' trial process is such that the defendant is already determined to be guilty by automatic verdict when he is arrested. (The Cardassians likewise.) The Federation would never allow an extradition under those circumstances, where the defendant has already been pronounced guilty by rule of process, since it goes against the Federation's core beliefs regarding justice. Thus Worf's extradition hearing would not even take place, and the Klingons' request would be summarily denied. Such extradition denial (often due to lack of an agreement because of an unfair judicial process) has been mentioned or taken place on previous (and subsequent) Star Trek episodes, with both Klingon and other worlds.
Worf says during his testimony that there is nothing honorable about attacking an opponent who cannot defend themselves, yet previously he was said to enjoy a holo-novel program based on Emporer Sompek, who did just that after the Battle of Tong Vey.
The model of the Miranda-class vessel in Captain Sisko's office moves from the left side of the office to the right.
Ch'Pok asks Chief O'Brian if he would have been the one to take command of the bridge if Commander Worf had been injured or killed, and O'Brian says yes. However Major Kira was on the bridge as well, as she is the station's first officer and carries the rank of Major (equal to the Starfleet rank of Lieutenant Commander), she would have been the one to take command of the Defiant in that event. Plus as O'Brian is a non-commissioned officer every other officer on the bridge outranked him.
The Klingon advocate asks Worf if he wept for those he'd killed. It was established in Star Trek VI that Klingons cannot shed tears for the dead, as they have no tear ducts.
While testifying and speaking directly to the camera, Chief O'Brien is seen wearing his standard duty uniform bearing the rank insignia of a Senior Chief Petty Officer. Moments later, in the courtroom, his dress uniform bears the single hollow pip he wore prior to DS9: "Hippocratic Oath".
If the importance of Worf's hearing was great enough to send an Admiral to adjudicate the matter, it would seem reasonable Worf would have been provided with a JAG Counsel instead of a serving officer.
At the trial's start, Ch'Pok accepts that all the facts given by Worf and other Starfleet officers aboard the Defiant during the incident were true, and states he wishes instead to prove that Worf had a secondary motive for attacking the transport ship. During O'Brien's testimony one fact Ch'Pok accepts without question is that Worf fired on the transport as it was decloaking, and did not know its identity but assumed it was the warship. Ch'Pok gets O'Brien to admit he himself would have waited for the ship to fully decloak before firing, suggesting Worf was negligent. Yet establishing that Worf did not know the identity of the ship destroys Ch'Pok's argument, which is that Worf fired on an unarmed ship carrying civilians on purpose.
The Klingon advocate bring up the Battle of Tong Vey, after which Emperor Sompek ordered the slaughter of an entire city, including civilians, women, and children. Sompek is referred to as one of the Klingon Empire's greatest heroes for this battle. Slaughtering unarmed civilians is gravely dishonorable, even cowardly. No warrior who did it would be considered heroic, and no great warrior would view such actions with any measure of respect.
Worf's baldric disappears after his first courtroom session. Clearly he is allowed to wear it, or else he'd have been forced to remove it before the trial began. As a big part of the issue is his pride at being a Klingon, removing it makes no sense.
The incident was a battle, and the Klingons were the attackers. The point of contention is that Commander Worf, as acting Captain of the Federation ship Defiant, after detecting the regular pattern of the two Klingon warships repeatedly decloaking right in front of them and firing on the Defiant and the Federation's unarmed civilian freighters (carrying medical supplies which the Defiant was sent to guard and protect fearing such an attack), Worf detected yet another decloaking in the same place and fired on them first before the decloaking Klingon ship could, but it turned out to be a Klingon civilian freighter. Considering the likelihood that a Klingon freighter would have weapons as well, and the unlikelihood that a civilian freighter would have a cloaking device, features that Worf knew, Worf acted as a good Captain should, in such a battle situation, by making an immediate decision to fire first that time. The fact that it turned out to be a civilian freighter is irrelevant. The Klingons were the aggressors by already firing on the Federation's civilian freighters, but nobody brings up this very obvious point.
During his testimony, O'Brien states that, had Worf been incapacitated, he would have assumed command of the Defiant. O'Brien is a non-commissioned crewman and is technically outranked by every commissioned officer onboard (his authority in the engineering department comes from his position as Chief Engineer, not his rank). Furthermore, Major Kira is aboard the Defiant at the time, and has been seen taking command on numerous occasions when O'Brien was also present.
Sisko asks Odo to use his previously-unmentioned contacts within the Klingon Empire to gather evidence for the trial, yet never asks Dax, who it is well established has many contacts within the empire, a number of whom owe her favors.
After Worf attacks Ch'Pok, Ch'Pok claims Worf said he would never attack an unarmed man. While that is true to the letter of what Worf said, it is disingenuous to the spirit of it. An honorable Klingon warrior would never attack an unarmed person with a weapon (or an unarmed ship with a warship like the Defiant), as that would be unfair and thus dishonorable. Worf struck Ch'Pok with his bare hands, thus both sides of the conflict were equally equipped and the combat was fair and honorable. Given that Ch'Pok's entire argument in the case was in regards to what was in Worf's heart, rather than the cold facts, his arguing semantics here is disingenuous at best.
Sisko never bothers to ask why a civilian transport ship would have a cloaking device.
Ch'Pok claims Chief O'Brien has been in Starfleet for 22 years, has been in 235 combat situations, and has been decorated 15 times. O'Brien does not disagree with him (though he says he thinks he's been in 100-150 combat situations). These statistics seem unlikely and improbably inflated, especially for an enlisted man who never advanced to a full officer.