When Sam is in the elevator, she starts on the 19th floor and, when she gets to 22, the elevator stops and she pounds on the door. Daniel hears her but he is on the 28th floor. Unless the elevator went from floor 22 to 28 in a half a second, there is no way Daniel could help Sam.
When Daniel (Michael Shanks) is explaining some of the writing on the orb to Carter (Amanda Tapping) he opens a small window with three characters in it. Then, he closes the window. Jack (Richard Dean Anderson) comes in and informs them it is morning. The camera point of view changes to show Daniel's computer and the window is now open again.
Jack sustains serious trauma to his left shoulder by having an inch thick rod go through it yet he has full mobility and never seems to suffer from the injury for the rest of his life.
This was deliberate on the orb's part, as it needed an interface to communicate. Frasier even comments on the absence of trauma. The organisms either somehow pushed his tissue cleanly to the side and/or healed the wound on the way out. Since the spikes do not fit normally inside the orb, reorganizing matter is easily within its capability.
The Stargate address when dialing P5C-353 is the same as Abydos in previous episodes.
Although the rod through Jack's shoulder is said to be embedded in the concrete behind him, it moves in reference to the wall when he does.
The orb shoots rods into concrete. They appear to be completely straight and rigid. However, the one which pierces the colonel's shoulder can be clearly seen bending. Therefore, it is made of something far more pliable than all the other rods. For example, it may be wood, fiberglass or plastic
which is then painted the same bronze like color as the rest of the device.
A camera view looking down at the "descending" lift actually shows an ascending lift. There is a looping cable visibly defying gravity "above" the lift. This same mistake happened previously in the pilot, Children of the Gods (1997).
After the organism gives back control of the computers and they begin the dialing sequence, there is no reason for them to not stop the auto-destruct immediately. The detonation is not a threat to the organism. Indeed it would benefit it by feeding it. The only threat is to the SGC and the planet, and it makes no sense for them not to stop it as soon as they are able, once the organism has agreed to leave.