Other mistake: In Shepard's apartment, there is a fresh pineapple and other fruit in his kitchen. This despite him having been in Atlantis for several months. This later turns out to be an artificial reality, but that should've been a big hint.
Other mistake: When the gate is activated (after O'Neill tells Woosley about the order to nuke the city), a member of the Atlantis team is on the bottom right, even though the Replicators have control of the city and no one from the Atlantis team is in the control room. This is because it's a reused establishing shot used throughout the series, including the series finale when the gate is activated (after Harriman says the Earth Stargate is offline).
Other mistake: McKay and Jackson enters a room and runs into 2 armored figures, Jackson eventually reveals that they are empty suits, however in every shot shot from behind the suits, the suits are constantly moving, as if they are hanging on strings.
Chosen answer: Because the ZPM allowing them to dial Atlantis was being used at the Antarctic defense outpost. They couldn't risk making Earth vulnerable to attack from Anubis by depleting it with repeated dialing to the Pegasus galaxy. Once they knew Atlantis was in serious danger, they had no choice.
Grumpy Scot
ZPM from Antarctic was depleted in first dial, dial in Siege was done via ZPM from Egypt (SG-1: Moebius Part-1/2).