When General O'Neill has to release the dead man's switch to drain the water from the Jumper bay, the third time he swims down, as he approaches the console he pushes on the switch, the camera closes in tight and he has yet to reach the console. While he may have let go and swam around, the switch was a slow release, so it should have still been pushed forward.
When the Replicators detected the Daedalus to raise the shield, this could only have happened after the ship came out of hyperspace. After the shield has been raised, the Atlantis team contact the Daedalus which is shown to be still traveling in hyperspace. It is established on the show that you can not detect or communicate with ships traveling in hyperspace.
O'Neill wears the wrong rank insignia. He wears one star of a Brigadier General, when he should be wearing two stars of a Major General.
Rodney states that, with the Jumper's cloaking device not functioning, there was no way to get close to Atlantis without being seen. However, in Grace Under Pressure (2005), it is established that jumpers are able to function underwater as submersible vehicles. They could have simply approached the city underwater to avoid detection while the city's sensors were down.
When Sheppard gives his authentication code to General O'Neill, when he first arrives in the puddle jumper, he states A6DC9; however, when he gives his authentication code to the Daedalus, he states ADC96.
Throughout the show, the Daedalus has been pronounced Dead-alus, however the actor playing the Replicator Cetus mispronounces it as Day-dalus. Technically, however, both pronunciations are incorrect, since the æ in Dædalus is correctly pronounced like the a in "cat."