Deliberate mistake: The dying Vantika hides his consciousness away in a portion of Dr. Bashir's mind. At one point, "Bashir" (heavily cloaked in clothing and shadows) comes up behind Quark and makes sure his demands are clear. At this point, it should still be unclear just how Vantika is still "alive", and whose body he is using. However, when he shoves Quark away, for a fraction of a second, Bashir's face can be seen under his hood. They were true to plot in using the right actor (though he shouldn't have been seen), it is possible some might have spied the secret earlier than the show meant to reveal it.
Continuity mistake: At the end of the episode, Odo has sent everyone affected by the telepathic matrix to a cargo bay. Sisko and O'Brien remove their com badges, throwing them aside before heading to the bay. After everyone is cured, Sisko straightens back up and, in the closeup, you can see that he has a badge on. In the next closeup, it's gone again.
Character mistake: When Nedelle collapses, everyone looks to Jadzia to save her and she says she can't. Why do they think Jadzia can save her? She isn't a doctor, and the Dax symbiant was never a doctor either. They are on board a Federation ship, with a Federation crew, why do they not call The Ship's doctor?
Plot hole: Just after the Kelleran soldiers kill all the scientists, O'Brien tries to contact the runabout Ganges for a beam out. Unable to contact the Ganges, he and Bashir use the T'Lani cruiser's transporter to beam down to T'Lani III. He could have used the cruiser's transporters to beam to the Ganges instead (it wouldn't have had its shields up as it was unoccupied and was closer to the cruiser than the planet) allowing them to escape back to the wormhole and DS9, instead of having to await rescue on the planet.
Other mistake: During the battle near the end of the episode, Sisko is heard saying, "Locking onto the lead ship" but he gives the firing order to Bashir, who is seated at the helm. This implies that the targeting controls and firing controls are at separate stations, which makes no sense.
Plot hole: Thomas Riker is able to steal the Defiant partially because he's a genetic double for and not a clone of Will Riker. Thomas Riker's existence is not a secret. Star Fleet is aware that the first officer of their flagship has a genetic duplicate who resigned and is out there somewhere. There should be something in place to verify Will's location before giving Thomas access. But then, of course, we wouldn't have an episode.
Plot hole: Earlier in the season, it was established that The Jem'Hadar are genetically engineered to be loyal to the Changelings, meaning they will not deliberately harm them. With that in mind, the Changelings still care about Odo's well being despite his refusal to return to them. So why didn't the Lovok Changeling send a message to The Jem'Hadar ships to inform them that a Changeling was going to be on the runabout? Given that he took time to offer another chance to return to his people, you would think he'd take time to make sure he returned to the station safely.
Character mistake: During the Defiant's flight to save the Cardassian officials, Worf says something to the effect of, "I've never been aboard a Federation ship equipped with a cloak before". However, he was aboard the Enterprise during the Pegasus incident, where The Ship was temporarily equipped with a cloaking device.