When the Dominion fleet is not visible at the coordinates the station's sensors indicate, O'Brien suggest they could be cloaked. Sisko says he didn't know the Dominion had cloaking technology. Sisko and Odo had suggested the possibility of the Dominion having reverse-engineered Romulan cloaking technology in season 4's "Homefront."
The "panel removal tool" is secreted under the pillow side of the mattress as the characters wait for the all-clear signal. Later, Dr. Bashir removes the tool from the opposite end of the cot.
The computer indicates that Dr. Bashir (really a changeling disguised as Bashir) was last located at runabout pad E. Runabout docking pads are usually numbered, not lettered, and there are only 3 of them. There would be no runabout pad E.
General Martok tells Bashir to bind Worf's broken ribs. This is not even done in the 20th century on Earth because it causes the patient to breathe very shallowly and risks contracting pneumonia.
Twice, Gowron ratifies documents by placing his thumbprint on them. Both times, it can be seen that he is just pressing his thumb against a random part of the prop. The first time, his thumb is over part of a block of text, the second time it is in the upper corner of an image of the Federation seal.
A previously unseen Romulan prisoner randomly appears in the closed barracks room just in time to be killed by the Jem'Hadar as an example to Bashir. Apparently the characters' plot armor is so thick it can generation disposable extras to die in the heroes' stead.
When the Romulan fleet first de-cloaks near the station, there are 4 identical Warbirds along the top of the screen. Everything about them is identical, including the size, movement, and angle of the ship in relation to the camera. Clearly only one model was shot for the scene and then pasted into the frame repeatedly.
Jadzia wasn't saying a ship could not go to warp inside a solar system, she was just saying it is risky and not a good idea. In fact in Star Trek: The Motion Picture (1979) Kirk mentions that it is a risk to go to warp while still in the solar system, but yet there are other times when they do go to warp in solar systems. While it is never explained on screen, the novels give an explanation for why some solar systems are dangerous to go through at warp, but other times not. It is dangerous to go to warp inside solar systems that have a lot of space traffic, like the Sol system or the Bajoran solar system, too great a risk of colliding with another ship. Also it is risky to use warp drive to travel from one point in a solar system to another point in it, as it requires precise navigation and timing. Using warp drive in a solar system that does not have space traffic, like one that is not inhabited by a space faring civilization is safe enough, but even then in this type of solar system it is recommended to not go above warp one until the ship has left the solar system because of potential hazards like comets and asteroids.
The changeling impersonated Dr. Bashir for over a month, interacting with the station crew many times, including Odo. Odo was previously able to detect the presence of other changelings, even when disguised as Starfleet officers, for example in season 4's "Homefront."
There is no reason for the Dominion to have the Runabout that Worf and Garak were captured in to be parked in orbit over the internment camp. It would've made more sense to destroy it, or at the very least, study it to figure out weaknesses in Federation technology.
After the prisoners escape the Jem'Hadar prison camp, they head back to the wormhole at maximum warp. A Starfleet runabout has a maximum speed of warp 5, while a Jem'Hadar fighter can travel warp 9.6. The Jem'Hadar should have easily been able to catch up to the runabout before it reached the wormhole, even with a significant head start.
So what was the changeling Bashir's plan. Was this a suicide mission. If not how was he escaping before he made the sun go super nova.
Dax objects to going to warp inside a solar system because it is hazardous. Throughout the Star Trek franchise, ships routinely go to warp inside solar systems. This objection is never brought up before or after.
The newly-arrived Romulan fleet requests permission to join the Starfleet and Klingon forces, which Captain Sisko grants. It was previously mentioned that a Admiral Gilhouly was in charge of the Starfleet task force, and Emperor Gowron is heading the Klingon fleet. Both outrank Sisko and should have been the ones coordinating such permissions.
Quark fears for the future of his business if the Dominion overtake the station, as the Jem'Hadar and founders do not eat, drink, or have sex. This ignores the fact that the Cardassians have just joined the Dominion, and the Dominion is only attempting to take the station at the Cardassians' behest. Quark profitably operated his bar under Cardassian oversight for many years before the station was turned over to the Bajorans and Federation.
After O'Brien is informed that the real Bashir has been away for 4 weeks, he says that he's been "hanging around with a changeling for over a month." 4 weeks is 28 days, while most months have 30 or 31 days. Even the shortest month, February, has 28 days (29 in a leap yer), so that is still not "over a month."
Dr. Bashir wields a makeshift knife and stabs a Jem'Hadar to death with it. This is a violation of his Hippocratic Oath.
When searching the barracks for Garak, one of the Jem'Hadar soldiers lifts the Breen's mattress to look under it. The mattress is very thin and resting on a cot frame. There is no way a person could be hiding between the mattress and the frame. The Jem'Hadar are meant to be obsessive and obedient, but not that dim.