During the pre-credit sequence, when Data and Wesley Crusher enter the bridge, Data declines the offer to pilot the ship into orbit. There follows a short cut-away showing an unknown crew member leaving the con so that Wesley can sit in the chair she occupied to pilot the craft himself. The crew member is clearly shown behind Wesley starting to proceed up the ramp towards the back of the bridge, yet when the camera switches back to Riker, Data and Picard, the crew member is not shown to walk behind them.
Data shows Crusher his hidden on/off switch, located on his right rib cage. But when Lore re-activates him later, he pushes a button hidden on Data's left side.
Towards the end, Lore is in the cargo hangar and Data, Crusher and Wesley arrive. They do not wait for security nor communicate with security, which would be a breach of protocol. It also takes a convenient amount of time for security to arrive.
The scene after the opening credits you can hear Riker say "Completely world, down to lifeless vegetation, no insects, not even soil bacteria" then a few moments later, Geordi say, "soils appears almost completely lifeless" Either it is completely lifeless or it is almost completely lifeless". Moreover, the term "lifeless vegetation" is odd. Taken literally, it means that there were plants but they are now all dead.
When Data is holding Lore's head, there is a visible seam running up the side of the neck (a remnant of the molding process used to create the prop). No such seam line exists when Lore is reassembled and activated.
Data states that he was found on Omicron Theta but this doesn't correspond to astronomical nomenclature (which Star Trek normally abides by well). A single Greek letter, followed by the name of the constellation as seen from Earth, is used singly to specify a star, such as Alpha Orionis or Theta Orionis, both in Orion. A planet is specified by a number after the star's name, e.g., Theta Orionis 3.
When Lore is lying on the bio-bed, with the crew lamenting that there has been no sign of consciousness yet, his eyelids can be seen fluttering.
Obvious use of photo/stunt doubles during the tussle between Data and Lore in the cargo bay.
When Data and Lore are seen from behind, it is easy to distinguish which is which. The photo-double used has a differently shaped head and neck and the wig is bulkier and longer.
When Riker activates the lights in the underground laboratory, the back wall of the hallway they are in is a painting used to extend the set and make it appear as though the hallway stretches much further than it does. The perspective does not quite align with the camera angle.
When Data fights with Lore, and manages to force him to throw the phaser away, it lands onto the transporter pad and breaks into two pieces.
No one on the bridge believes Wesley that something is off with "Data" (actually Lore in disguise), yet Crusher follows him to Data's quarters and immediately believes that the unconscious android on the floor is Data, even though Riker had seemingly confirmed it to be Lore.
Data states that he was found on the surface of Omicron Theta "26 years ago". The first season of TNG takes place in the year 2364, which would imply that Data was found in the year 2338. Yet in the pilot Encounter at Farpoint (1987), Data tells Commander Riker that he graduated from Starfleet Academy "Class of '78", which would imply 2278--a full 60 years before Data was found. Since the 2364 date was not established until the Season One finale The Neutral Zone (1988), it is feasible that such an error could not have been predicted at the time.
The Crystalline Entity is a known destroyer of colonies and worlds, yet at the end of the episode, the Enterprise does nothing to pursue, track, or destroy the creature, nor is any mention made of warning other worlds or ships about it. Instead, they let it go, and go off in a different direction.
Lore is said, and shown, to be much better at understanding and "handling" humans than Data, easily manipulating them and interacting casually. Yet when he recommends a course of action and Picard tells him to, "Make it so," he is confused by the rather self-explanatory phrase.
The away team, especially Riker, seem surprised when Data brings up Dr. Soong and names him as his creator, seemingly a new bit of information about Data's past that has been unlocked from his memories. Data is made in the exact image of Dr. Soong. (Both are played by Brent Spiner.) Surely someone in the 26 years since Data was found would have made the connection between the Federation's foremost robotics expert and an android that is his physical double.
Picard orders Yar to take a team to the cargo bay and observe Lore (disguised as Data). Wesley and Beverly make a side trip to Data's quarters, reactivate the real Data, and arrive in the cargo bay before any security force.
Data has pointed sideburns, which are a tradition among male Starfleet officers. There is no reason that Lore would have the same hairstyle, especially given Dr. Soong's dislike/distrust of the Federation, other than so he would more closely resemble Data and be able to switch places with him.
After Lore has been transported off and Picard addresses Data asking 'Data, you all right?'. Data answers, 'Yes, sir. I'm fine', yet Data is not supposed to be able to use contractions.
At the beginning of the episode, Picard announces the stardate as 41242.4. After the opening credits, Riker uses a stardate of 4124.5, leaving out a digit.
When Data first discovers Lore's body components, he has a very emotional response to this, such as when real humans discover a long-lost relative.
When the crystal entity is first detected, Geordi says that it's coming in on a "5 o'clock tangent." As Geordi explained to Lore earlier, the Enterprise moves through 3-dimensional space and requires more complex coordinates (two bearings separated by the term "mark"). The traditional method of describing an object's location to one's self using a clock face as reference only accounts for a 2 dimensional plane.
When the crystalline entity is attacking the Enterprise, Yar announce that, "Deflector shields are holding." Deflectors refer to the low-grade field that surrounds the ship to protect it from space debris as it travels. Shields are the fully-powered energy barrier that protects the ship from stronger attacks. Picard had earlier ordered a yellow alert status called and the shields raised. The visual effects of the attack show that the full shields are active.