When Dr. Weir is standing on one of Atlantis' outside balconies at night the Big Dipper constellation can be seen in the background. This would not be possible as Atlantis is in the Pegasus Dwarf Galaxy, which is over 3,100,000 light-years from Earth; the stars that make up the Big Dipper are not only all located within the Milky Way Galaxy, they are all in the same quadrant of the galaxy, and range between 79 and 124 light-years from Earth. They would not be able to be seen from the Pegasus Galaxy with the naked eye and if viewed through a telescope would appear in a completely different configuration from the Pegasus Galaxy.
When the Orion emerged from hyperspace, it would not have had enough velocity to maintain orbit therefore it would have immediately plunged back to the planet.
Doctor Beckett states that the stargate was swallowed up by magma. However, as it was on the surface of the planet, he should have said that it was lava, not magma. Magma is underground, lava is above ground. However, it must be noted that Beckett is a Medical Doctor and not everyone is aware of the distinction between magma and lava. Moreover, when the stargate was 'swallowed', it went underground, i.e., into magma.
Instead of loading up the Daedalus and transporting everyone back to Atlantis, they could have used the ship's beaming technology to beam everyone to another part of the world where they could survive the initial eruption. Then, after getting everyone out of the initial eruption area, they could have ferried everyone back to Atlantis without the time constraint.