Bashir speaks with a couple of different representatives of Starfleet Medical via subspace. One even has the caduceus symbol on the wall behind him, to drive home the point that he works in the medical branch. Both are seen wearing red Starfleet uniforms. Starfleet Medical personnel, regardless of rank or position, wear blue uniforms.
The "goo" coming off Odo is its usual opaque, viscous consistency, yet when it's seen in Dr. Bashir's beaker, it is thin, transparent, and more yellowy than usual. This cannot be a result of the morphogenic virus in his system, as that has been shown to turn a changeling's liquid form black, not thin and yellow.
The pages of text in the Book of the Kosst Amojan are clearly printed on paper that was then adhered to the actual pages of the prop book, likely because only one copy of the prop was fabricated and the pages needed to appear blank throughout "The Changing Face of Evil."
The bottom edge of the star field screen can been seen at the bottom of the window in Captain Sisko's office as it slowly moves from right to left at 0:02:42 during the cold open.
As the representative of Starfleet Medical points out, Bashir has performed his own scans of Odo over the years. Bashir states he wants Starfleet Medical's to use as a point of comparison to his most recent scan. Bashir's own previous scans would function just as well as Starfleet Medical's.
After Kira is given a Starfleet commission, Garak is seen tailoring her uniform. Garak is an independent merchant and Starfleet clearly has its own methods of fabricating and distributing uniforms. There is no reason her uniform would be made by an outside party, which would make it something of a bootleg, when the whole point of the Starfleet commission is to iterate her authority as a legitimate representative of the Federation.
Bashir traces the progression of the virus in Odo's system to pinpoint the exact stardate on which he was infected. It doesn't seem to take into account that Odo's morphogenic matrix was forcibly removed and he was made into a "solid" for many months. Even if the virus was still in his system after he merged with the infant changeling and became a metamorph again, the progression of the virus would have undoubtedly been altered.
Dukat was sent by the Pah-wraiths to guide Kai Winn, and at one point served as the host for the Pah-wraith Kosst Amojan. There's no reason for the Pah-wraiths to punish him with blindness for attempting to read the Book of the Kosst Amojan.
Bashir discussing Odo's medical condition with Chief O'Brien is a violation of patient confidentiality.
Dr. Bashir tells Odo with certainty that he has the morphogenic virus that has infected his people. No one from Starfleet has ever had a chance to study an infected changeling. They only know of the virus through word of mouth. At best, Bashir would be able to tell that something is wrong with Odo's morphogenic matrix and suspect that Odo is infected by the same disease, but as a man of science he would know that he cannot be 100% certain without a study of the other infected changelings.
Doctor Bashir tells Odo about the disease with several crew members present. This is a violation of patient privacy.
After Bashir notices that the file Starfleet Medical sent him of their alleged scans of Odo have the same resonance dispersal patterns as the ones he received from Dr. Mora when he first came to the station, O'Brien questions whether two scans can have the same dispersal pattern. O'Brien may not be a doctor, but he is an engineer. He knows how scanners work.
Gul Rusot scoffs at the idea of Federation food replicators being used as a resource. Replicators simply create foodstuff from raw molecular material in a pre-programmed recipe. As long as they are programmed with Cardassian recipes, which they easily could be, then the resulting product would be indistinguishable regardless of who manufactured the replicator.