Why would Sloane put his entire collection of Rambaldi serum out in the open where it could potentially be compromised? It's been established that Sloane is not dumb and well versed in Game theory. Even a novice in Game theory or contingencies would keep something that valuable in a spot that isn't easily reached or at the very least, easily compromised/broken, yet Nadia is able to destroy them quickly and conveniently.
If The Passenger was already known to the Russians, and they did experiments on her with the Rambaldi serum, why did everyone go through the trouble of collecting the Rambaldi artifacts to build "Il Dire", that's the final machine that gave Sloane the word "Peace" and generated the genetic code in "Unveiled". Also, some of the artifacts used to build "Il Dire" where hidden and untouched for may years so how did the Russians know who the passenger was and what she represented?
When Vaughn, Sydney and Katya are driving away from the checkpoint outside of Novgorod 12, you can clearly see palm trees in the background. No species of palm tree grows in Russia.
How does Vaughn know there was acid in the beaker? He just picks up a glass rod and dips it in the acid, then puts it on Suit & Glasses. But the beaker is unmarked, and they didn't have a chance to see S&G use the acid.
Going into someone's safehouse and putting your fingerprints all over their secret cache of untraceable weapons isn't really a good idea. If Jack were to use one of those weapons down the road to kill someone, then Vaughn's fingerprints would be on them.
Why did they give Toni a gun for the break-in mission? Given she's a prisoner out on parole and all, and she really only needs to get in to deactivate the security system, arming her seems like a real dumb idea.
Why did Sloane let Lauren and Sark get anywhere close to his secret Japanese base with a rocket launcher?!? Didn't he bother to search their vehicle? All they had to do was fire at his house as they were leaving, once they had the Rimbaldi info. Sloane didn't anticipate something like that?
At the end when Vaughn is in Jack's Weapon-Chamber he looks through a sniper-rifle with Scope. But he only opened the rear of the Scope and forgot the front. No wonder he always misses Lauren.
According to Brill, Bill Vaughn was killed by Irina after he rescued Nadia from the custody of the KGB. But now Katya says that Nadia was born after Irina faked her death, which means that Irina would have had to kill Bill Vaughn after she was supposedly dead; but all Jack, Devlin, and the various other CIA senior officers knew that Irina killed Bill Vaughn, so wouldn't they also have known that Irina was still alive? Of course, either Brill or Katya could be lying.
Number 47: (inverted) Marshall says that they got the surveillance footage from 74th.
Sloane explains why he injected himself with the green fluid in "After Six."
In the scene where Vaughn leaves the elevator after the meeting with Brill, you can see that someone is standing in the right corner see screenshot.
Number 47: Sloane says that he has 72 hours to live and that he had an affair 25 years ago, 72 minus 25 equals 47.
Vaughn sneaking around while visiting Lauren's house in Richmond is very similar to Sydney getting page 47 out of Sloane's house in season one. Both items were locked in a safe.
Jack and Sloane were both in Saigon 1975.
Vaughn scans the manuscript in the safe top to bottom, but when Marshall receives them at the other end, he gets them being scanned left-to-right.
Sloane mentions taking a bullet for Jack in "Breaking Point."
Lauren dropped a piece of note into a garbage can is very much like how Sydney and the real CIA communicate during the first season. Of course, Vaughn took the note out of the trash and found that it was simply a to-do list.
Only one item on the list was checked, and it was to "pay the bills". Vaughn being the intelligent officer that he is should have kept the list for himself - in case it was some coded message for someone from the Covenant to obtain. He should know.
Besides, why would Lauren discard a list that still had items unchecked? Logically, she still needs to do them, cause almost all were unchecked.
Flash drives (such as the USB memory stick that the data was on) are not vulnerable to magnetic fields, and an EMP strong enough to wipe the drive would also have fried the computer in a very obvious way. A strong enough X-ray beam could mess up the data, but probably also given the wearer of the ring cancer in short order. The explanation of solar flare activity is just nonsense (unless of course you were in a high earth orbit).
When Vaughn discovers the safe room door in Dr. Viadro's house, the keypad LEDs show it to be unlocked (one green LED). But when he approaches the keypad to to attempt a circumvent of the electronics, the LEDs indicate it is in a locked state again (two red LEDs).