Zelenka has a control crystal in his space-suited hand while talking with Sheppard after he has been injured with a micro-asteroid. The next scene shows Sheppard helping Zelenka finish his task and no crystal in his hand.
Atlantis is seen drifting through space with the city perpendicular to the direction of motion. However, the star drive propels the city from the bottom, and therefore should be seen with its vertical axis parallel to the line of motion, since the drive failed and there was no mention (let alone power or reason) to change the city's orientation after it had fallen out of hyperspace.
There is no need for the puddle jumpers to make passes through the asteroid belt as if they are on strafing runs. Since they are in space and do not need forward momentum to continue flying, they would simply hover in front of the asteroid belt and destroy the asteroids.
Around 21 minutes, when the jumper bay door opens to let the jumpers out, there is what appears to be sunlight shining on the outer exit yet it is almost completely dark outside since they are adrift in deep space.
Lettering is reversed on Zelenka's spacesuit as he and Sheppard prepare for the space jump. However, on spacesuits, lettering is normally reversed on the torso markings to allow reading by the astronaut via mirrors on the spacesuit's sleeves.
Rodney McKay mentions once having scored 0 in the video game Asteroids (1979). This is impossible, as every death in Asteroids nets at least 25 points. (You get 25 points minimum for colliding with a large asteroid or alien projectile.) The minimum score (with 3 starting lives) is therefore 75 points. Actually it is possible to score zero if shot down by the saucer three times.
When the team goes out in the puddle jumpers to blast the asteroids, an Apollo pilot has a Daedalus patch on his uniform. However, it has been previously established that some Apollo crew were temporarily seconded to the Daedalus.
When Zelenka and Sheppard see that the hall is missing to the array, Sheppard uses forward momentum to throw themselves across the gap. The moment they demagnetized their boots, the city-ship should have flew past them. Much more likely is that they would have been ripped from their magnet boots.
Their forward momentum is the same as the city's. In a vacuum (with no air resistance to pull them), when their boots are demagnetized, they would continue to travel at the same speed as the city.
Colonel Ellis is able to dial a Stargate and have 2-way communication with the Midway station. In S03E10 - The Return, it's established that Midway is too far to dial directly, and instead other gates along the way store their buffer and dial the next gate. Two way communication would not be possible with this technique.
Dr. Keller performs CPR on Elizabeth while moving down the hallway, but her hand placement is incorrect. Her hands are near the top of the sternum, above the breasts, when they should be at the lower half of the sternum, between or below the breasts.