Toward the end of the fight in Ops, Dax can be seen fighting off a group of Klingons with a Bat'leth. The scene cuts to Sisko with his own Bat'leth, then pans to Dax; however, her Bat'leth is nowhere to be found.
While Worf is fighting the holographic alien in the training program on the holosuite, his mek'leth appears to be bent when seen from the rear of the alien, but straight when seen from the rear of Worf.
After the Klingons have invaded the station, Worf's mek'leth appears out of nowhere. He doesn't have it one moment, then the next it is in his hand. He was not seen carrying it earlier, and it is far too large of a weapon for him to have been concealing it on his person.
Quark claims that the ambient noise level in the bar is less than 30 decibels. In the decibel scale, normal conversation is rated at 60 db and a quiet whisper can be as little as 20 db. Given that Quark and the others are speaking normally, the ambient level is significantly higher than 30 db, and in a crowded bar, could be as high as 90 - 100 db.
The Defiant is said to have been equipped with ablative armor that protects the ship even with the shields lowered. Ablative armor works by burning off its outer layers in a controlled manner to protect the layers of plating beneath it. No such burning effect is visible on the hull of the Defiant.
Garak's circular, central forehead ridge is incorrectly colored blue (a female color) in an early scene where he and Odo confront a group of Klingons and again when he is in the infirmary.
After the Defiant rescues Dukat and the council, Captain Sisko orders Dax to raise the ship's shields and activate the cloak before she notifies him the latter was offline as they go to warp. But it's been indicated that shields cannot be utilized while a ship is under cloak.
During the fight scene in Ops, Worf is seen fighting a Klingon attacker; behind him, another Klingon can be seen fighting an invisible opponent.
After Garak has tried the root beer, Quark describes it as bubbly, happy, and cloying. The drink that Quark served Garak was flat, not bubbly.
Several of the Klingon ships that are destroyed explode with no debris. One moment they're a ship, the next they're fiery vapor.
When Gowron invites Worf to the invasion of Cardassia, he smacks Worf on the chest. This causes his communicator to rotate 45 degrees. In the very next cut back to Worf in the same conversation, the badge is again correctly oriented.
Several times, Klingonese is spoken and needs to be translated for the Starfleet/Bajoran officers by either Worf or Dax. All Starfleet and Bajoran personnel are equipped with a universal translator in the combadge, which is presumably how they understand most of what the Klingons say. There is no reason that a few simple phrases should go untranslated and require a native/fluid speaker to interpret.
Klingon warriors are meant to be some of the fiercest, most skilled fighters in the galaxy, not to mention much stronger than most species (including humans and Bajorans). Yet the Klingons that invade Deep Space Nine are all easily bested in combat, even by Major Kira after she receives a knife wound to the back.
After the station's shields are weakened and Klingon boarding parties beam aboard, the entire ops crew is engaged in hand-to-hand combat. No one is manning the station's weapons, yet the Klingon ships do not take advantage of this large opening.
Garak, Dukat, and a pair of Starfleet security officers position themselves outside of the guest quarters containing the Cardassian ruling council members, prepared to defend them in case of a Klingon invasion. The Klingons board the station using transporters. Having security personnel outside the council's quarters won't be of much help should the Klingons decide to just beam into their quarters.
At the end of the Episode Worf mentions knowing nothing about Command, although when first introduced during Season 1 of Star Trek The Next Generation, he was a command officer before transferring to security after the Death of Tasha Yar, and yet he acts like he doesn't know anything about command, despite him having trained it at the Academy to become a command officer.
Sisko tells Worf to be on the lookout for Klingon ships, cloaked or otherwise. If the Klingon ships are cloaked, then the Defiant would not be able to detect them. That is the whole purpose of a cloaking device. If the implication is that Worf and/or Starfleet have a way to penetrate a ship's cloaking device anyway, then it would stand to reason that the reverse is also true: the Klingons would be able to detect the cloaked Defiant. This would be especially true since the Defiant is overpowered and its warp signature can be detected through its cloaking device if one knows what to look for.
Worf says that he had never been on a Federation starship with a cloaking device. In one of his previous adventures The Pegasus (1994), Enterprise-D was briefly outfitted with a "metaphasic" cloaking device, of a different type than the Defiant device but nevertheless a cloak.
Dr. Bashir refers to 2 decades of peace with the Klingons. Peace has existed between the Federation and Klingon Empire since the signing of the Khitomer Accords in 2293. As the events depicted here take place in 2372, that's nearly 8 decades of peace, not 2.
At the end, Worf is seen wearing a new uniform with the red shoulders, and O'Brien tells Worf how great he looks in red. Worf then replies "It feels good" as if this is the first time he has worn a uniform of this color. In the entire first season of "Star Trek The Next Generation", he wore red.