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: During the previous episode, we find out that Dr. Bashir has been replaced by a changeling. But for the changeling's ruse to work, he would need to carry out all Bashir's duties. Which means he'd need all his medical knowledge. Bashir graduated second in his class at Starfleet Medical Academy. To learn all that Bashir knew would have taken longer than the Dominion and Federation knew about each other. Not only that, but to pull off all this changeling pulled off, he'd need intimate knowledge of Starfleet, Bajoran and Cardassian technologies. There's no way a changeling could have learned all that knowledge in the time alotted. Even if you use the excuse of the Great Link, the Founders would still need the time to amass the knowledge and at least one of them to learn all the medical techniques Bashir would have known to transfer that knowledge to the others, otherwise it would have been a dead giveaway Bashir wasn't really Bashir.
Plot hole: Odo would have already been infected by the virus by this point. He passes the infection to The Great Link in episode 4-26. It's highly unlikely they would have found a cure on this planet with little medical supplies and the elder Odo never mentions it. Odo should not have survived to see the crew of the Defiant return.
Continuity mistake: During the roll call for the fight on the space station, some of the officer's shirts are different colors than the shirts used when they filmed the roll call in the original series.
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