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.
Suggested correction: At this point Thomas Riker is still a Starfleet officer. There is no need to lock him out of accessing the Defiant's systems as he is considered just as trustworthy as Will.
It's said that he resigned over suspected Maquis sympathies. They were right.
They say that he had expressed political opinions that supported the Maquis, not that he had resigned from Starfleet. A large number of Starfleet officers supported the Maquis' intentions, but still stayed loyal to Starfleet.
No, Thomas Riker accessed the Defiant under the guise of being Will Riker, and Major Kira released the lockouts being under that impression.
Exactly. NOBODY in Star Fleet has thought "Well, what if one of them claims to be the other? How do we tell them apart?"
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.
Suggested correction: Maybe The Jem'Hadar were trying to disable the runabout to try and capture Odo and Garak.
