Before Syd and Marshall used the eye to get in to the room with the firewall, but after they got off the elevator, Syd has a gun in her right hand in one shot and then comes around the corner in the next shot with no gun in hand.
Why the big drop off and where is Marshall's car? It's not like he drove it to Cuba, it must be somewhere local.
Wouldn't Marshall's wife be concerned about how he got home, considering he didn't come home in his car? How will he get to work the next day?
Goof: During the first conversation Roberto Fox has with Nadia, when she was in the cell, he uses words an Argentinian wouldn't normally use. He says "tienes" (have, in Spanish) instead of "tenes", and "tu" (you, in Spanish) instead of "vos". These expression are nearly exclusive to Argentinians. The language however is corrected in Roberto and Nadia's later conversations.
Sydney asks if Sam can drive the van, however she doesn't ask him if he can break into it and hotwire it.
Luckily, the door was unlocked and he finds the key above the sun visor.
It doesn't seem like she activates the helicopter on purpose, it looks like it just happens to activate when she looks at it - she doesn't even touch it.
I think the baddies unleash it on her after they see her trying to tamper with it. It isn't exactly a one-use weapon so they can afford to take her down with it and still have it in working condition.
When Sydney meets up with her contact and realizes it's a trap, she says she won't have supplies and then she and Sam run off to the Metro. Why doesn't Sydney grab what arms she can off the men she neutralized so she would at least have something? Rather than nothing.
Why doesn't Sydney have any weapons in the first place? She seems to be strangely unequipped for this mission.
Salzburg does not have a subway system.
Even after fully understanding the conventions and potential danger of the mini-helicopter, Sydney activates it for no good reason.
Marshall begins giving background information on Sam Hauser to Sydney without motivation.
In the opening scene when Sydney gets her Martini with 4 olives, she removes the olives (and puts them beside her drink), but in a following cut of the scene the olives are back in her drink.
Sloane said that 3 CIA analysts were killed when the Index was stolen, but the written briefing Dixon has when he meets Sydney in secret indicates that 4 agents were killed.
Goof: Chase tells Dixon that Sloane is authorized to contact his former associates. In the previous two episodes he had to step down as APO Director because the situation involved former associates.
One would assume that if Sloane were unable to contact any of his former associates he would be pretty useless at his job. In the previous episodes it was stated that Sloane could not have contact with a select number of his former associates who were on a list, including Anna Espinosa and Sark. It seems that the man he contacted in this episode is not on that list.
Number 47: When Dixon runs a backtrace on one of Sloane's calls it shows the address "Avdage Stepe 47".
Number 47: Sloane's vehicle ID shown in the satellite tracker is 30947 28436.
The dinner scene in Sloane's house is very similar to the one in season one's "Page 47."
The show revisits the false TV cliche that something can be put in a coin operated locker and will stay there indefinitely until someone with a key collects it. In truth these lockers are emptied regularly and if an item is left inside it is stored and the locker rekeyed, otherwise the operator would suffer financial loss, While as the story turns out in this case the envelope could have been placed in the locker in the last 24 hours, why did Vaughn just accept that the package was still in the locker when he got to it, if he thought his uncle placed it there?
Sydney welds through a metal grate and touches the metal immediately. Unless that was some sort of special CIA cool welder she should have been burned by the hot metal.
Goof: Near the end, Nadia crashes through the garage door of building 37 in the red Mustang. A few minutes later, the car is seen without a scratch.
When the overview of Brussels is shown, there are mountains in the background. In Belgium there aren't any mountains as high as those shown, and certainly not around Brussels. Also, the map indicating the "port area" isn't Brussels. Another detail: when you need a "fast car" in Europe, one wouldn't import an American Muscle Car for the occasion, but use what's at hand. So the Mustang isn't exactly in place. They did get the plates right, though. However, all the Belgian cars use the same plate.
Also, there is no Rue Voltaire in Brussels. There is only an Avenue Voltaire which is indeed close to the dockside.