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.
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.