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.
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.
Character mistake: At the end, Sisko blames the deaths of the runabout crew (Hoya, Rooney and Bertram) on himself and the Vorta not trusting each other. However, the runabout was destroyed before any negotiations had taken place, and even before any Jem'Hadar or Vorta had landed on the planet, so their deaths were largely unavoidable. Even the later deaths of T'Lor and Muniz were caused by the first firefight, again, before any negotiations had happened.
Other mistake: Sloan arrived at the station to destroy the cure, and he and Bashir discuss the fact Sloan has to know what it is to be able to find it in Bashir's lab to be able to get rid of it. Sloan counters he could destroy the whole lab, and Bashir dismisses this as not subtle enough for Sloan. Obviously they've both forgotten that Bashir has perfect memory, so he'd need to be killed to get rid of the cure as well, not just destroy the lab. Something which Bashir would have brought up to back his point up, or Sloan could have used to defend his idea, destroying the lab with Bashir inside, getting rid of both.
Factual error: When Major Kira was introducing Lieutenant Commanders Dax and Worf to the arriving Trill scientists, she introduces them as Commander Dax and Worf. While in informal conversation, they could be addressed as Commander, when making formal introductions, the person making the introductions would use their full proper rank. This is an error that no ranking officer would make, especially not twice. (00:03:10)