Revealing mistake: In the scene where Barclay reappears on the transporter with the crewmember, they both fall to the ground. The transporter chief had put up a forcefield around the transporter chamber, in case something goes wrong. However, when the crewmember falls to the ground, his foot goes right through where the forcefield is meant to be. It is still active, as only a few seconds later we see it being deactivated.
Visible crew/equipment: During Data's second dream experience he imagines becoming a bird and flies through the Enterprise and beyond. As he flies past his father Soong standing at the anvil, a crew member is sitting on the floor by the double doors behind him. This has been edited out in some versions. (00:36:10)
Continuity mistake: In the scene right before the shuttle's crew finds the Romulan ship and the Enterprise, Geordi calls the shuttle craft's cockpit to explain the temporal disturbances. Captain Picard, Troi and Data walk into the shuttle's cockpit room and Troi puts her right arm on Geordi's chair. As Geordi, Data and Captain Picard are talking you can see Troi's wrist hanging off the chair, but when the camera cuts directly in front of Geordi her whole wrist is on the chair. The camera then cuts back and you can see that Troi's wrist is still hanging off the chair.
Visible crew/equipment: In the scene where Picard comes to engineering to ask Laforge if he has been successful in locating Riker's homing beacon, you can see the blue light of the warp core reflected in the window. Outlined in that reflection, near Geordi's chest, you can see a studio spotlight.
Factual error: Picard reaches for the bowl of rotten fruit, winces in pain, and suddenly his fingernails have grown about an inch. This was due to the fruit bowl being inside an area where time was moving much faster. The problem is, in order for his fingernails to grow, blood would have to supply the needed nutrients to his fingers at the accelerated rate. Since his heart is in normal time, being away from the bowl of fruit, there is no way his fingernails could have grown like that - his heart is only supplying a normal-time-continuum's worth of blood.
Plot hole: During a private conversation with Worf, (the not yet revealed to be clone of) Kahless recounts a time during Worf's childhood when the actual Kahless appeared to Worf in a vision and told him he would do something no other Klingon had ever done. However, it would be impossible for a clone to have such a memory, as his creators would have no knowledge that such a memory even existed, let alone the circumstances and specific content of that vision.
Continuity mistake: The stardate given in the previous episode is 46578.4 and the stardate of the episode after this is 46682.4. In this episode, Picard records the stardate in his log as 46759.2. There was either a typo in the script or the actor misspoke the scripted 46579.2. This isn't excusable as a character error, because the episode is accepted in Trek lore as occurring on the date Picard states.
Continuity mistake: In the scene where Captain Picard reaches for the aged fruit, he screams while holding his right wrist with his left hand. As Troi, Geordi, and Data rush in you can see Captain Picard holding his wrist up in the air. The camera then cuts directly in front of Captain Picard and you can see Troi scanning his wrist but he isn't holding his wrist anymore. The camera then cuts directly in front of Troi and Geordi and you can see that Captain Picard is still holding his wrist. The camera then again cuts back to Captain Picard and he isn't holding his wrist anymore.
Factual error: With the Enterprise and the Romulan ship are stuck in a bubble in time and virtually stopped, the 2 ships would not be visible to the crew on the shuttle. The light entering the bubble would slow down, as would the light reflecting off the ships. All the shuttle crew would see is a "black hole" in space. (The disruptor beam was stopped in mid fire and sensors cannot penetrate the bubble).
Plot hole: About two thirds of the way through this episode, Data deduces how Moriarty was able to 'leave' the holodeck. The big reveal is that he never did leave the holodeck, he merely reprogrammed it to simulate the rest of the ship without Picard, Barclay or Data's knowledge. While it is believable that this would fool humans like Picard and Barclay, it is ludicrous to suggest that Data would be taken in by it, even for a second. Data is an android whose perceptions of sight, sound and the world around him are far more sophisticated than humans. To list what we know of Data's perceptive abilities from previous episodes would take up the entire page, but suffice it to say he should have immediately recognised the 'Enterprise' as force fields and holograms rather than the genuine article. Note: this goes beyond a 'character mistake' or anything like that. Data's enthusiasm for Sherlock Holmes style deduction should have led him to eliminate the impossible before considering what was probable. Data accepts the impossibility of a holodeck character existing is the real world before discounting the possibility that it was still a holodeck simulation. This contradicts an awful lot of what is known about Data's abilities and powers of deduction. Although it serves for a good mystery the fact is it takes Data far longer than it should to deduce, or even guess at, the truth of their situation.
Plot hole: When Picard, Geordi, and Troi encounter one of the first time disturbances it results in one of the runabout's nacelles using up all of its fuel. Data says this is due to it having been in operation for 47 days (according to the plasma conversion sensor). After this the Captain reaches for the bowl of rotting fruit which causes him to scream in pain. The other crew members rush in and Troi scans his hand. She tells Picard that his hand is metabolizing at approximately 50 times the normal rate. Data and Geordi then discover that the temporal disturbance which covers the fruit also covers the nacelle that has lost all of its fuel. Data also notes the disturbance extends outward from the hull, about 17 meters from the ship and is spherical in shape. The problem here is that according to what Data said earlier the engine was active for 47 days even though it had only very briefly come into contact with the time distortion - maybe 1 second at most, but likely far less time than this since the ship was at warp when the fuel was consumed. So if we assume the engine was in contact with the fragment for 1 second then time is actually moving at 4,060,800 times the normal rate - not 47 or 50 times normal. (00:11:00 - 00:12:00)