When Vaughn's in Khasinau's lab with the other bodies, Khasinau preps him with iodine. Later, after Sydney comes in and Khasinau hightails it out of there, the iodine on Vaughn's chest is suddenly gone. Unless it magically got wiped off completely in the space of about two seconds, there's some serious continuity going on.
Where in the world did Vaughn get a screwdriver when he was locked in a hallway with ultimately life-threatening liquid completely submerging him? And how did he manage to climb up that ventilation shaft with no footholds or climbing equipment.
In the first 5 minutes when Sydney is talking with her mom and they cut from Irina to Sydney you can tell they used shots from last season and new shots from this season because Sydney's blue wig is styled differently between shots. In some shots the hair is brushed under in other shots it hangs perfectly straight.
When Sydney is cutting a hole in the glass to climb in and steal the camera it is clearly shown that she does not cut a perfect circle. However, every other time we see the circle from then on it is a perfect circle.
The scene in which Sydney walks through CIA headquarters at the end of the episode mirrors the scene in which Sydney walks through SD-6 at the end of the pilot. In both sequences Sydney hands Sloane and Kendall something she recovered from a mission to gain their trust and in both she is wearing an alias.
When getting a long shot giving an introduction to Rabat, it actually is the well-known marketplace in Marrakech, Marocco.
When Sydney is talking to her mother through the glass wall of the cell, when the camera goes back and forth between Irina and Sydney, continuity errors are shown, as Sydney's hair is in front of her right ear, then behind, then in front of and so on.
Goof: When entering the CIA headquarters, Vaughn instructs Sydney to turn left after passing the intersection cameras. When they cut to the surveillance footage, you see Sydney arching to her right to cross the street.
When Sydney is in Helsinki, there are visible skyscrapers in the background. However, there are no skyscrapers in Helsinki.
Despite the fact we see Sydney putting on a big bandage on her shoulder gunshot wound, later in the episode when she's wearing the zebra-dress to get into the hotel in Rabat, it's nowhere in sight.
The list of Russian authors on Sark's laptop, Will saw during his hypnosis:
Goof: The luge sled is capable of speeds of up to 150 mph and she needs to go two miles in 12 seconds. At 150 mph, it would take her 48 seconds to go two miles.
The high-powered "luge" that Sydney uses to race the flames of the launch is shown to reach 125, whether that is mph or kph, which is a high speed. One would assume since she is racing for her life, that she isn't going to slow down even as she exits. As she exits the exhaust tunnel, she immediately "tucks, ducks and rolls" off of the "luge". Any motorcycle aficionado will tell you that isn't a smart move without plently of buffer between you and the concrete. The suit Sydney is wearing doesn't appear to be thick or leather, at the very least the suit should be in shreds and at worst, Sydney would be road taffy.
Goof: In the scene right after Sydney comes out of the exhaust tunnel with fire behind her, you can see the wire for the luge pulling her.
In a real satellite launch the payload (the satellite) would be very carefully wrapped in a cocoon at the very top of the rocket and be multiple layers deep into it. You would not be able to access it while on the launch-pad, let alone in a hurry. Satellites take months or years to assemble.
When touring the launch facility the greeter talks about how environmentally friendly the launch is, and how the propellent gas is processed. However the exhaust tube leads to an open-air area, and there is no evidence of any waste collection or the high volumes of water that are usually pumped into those areas to help keep down the heat.
When sitting outside the launch facility, Dixon is dressed in full camouflage, right down to the face paint, & sitting next to a tree, to further "blend in"... Then he opens his laptop, to gain access to the Launch Site's security camera's... He uses a Mac Powerbook because amidst all that Blending he opened a Bright silver laptop, with a Glowing Apple logo on the other side of the screen!
Goof: When Sydney is under the water and uses the tank from the dead man to get air, you see her white headband slip off her head. But in the next scene it is back in a snug position over her head. Obviously this is a goof, because at the time of trying to preserve one's life, the concern is hardly fashion.
Goof: The assault rifle would have jammed underwater.
Goof: Dixon said that the water was so cold that it would freeze in 4 seconds. If it was that cold she would freeze to death while she was under the ice.