When the real Jack is about the return through the Stargate, the iris is open. However, he could not have sent the GDO code to open the iris, because the gate is not open yet.
O'Neill's son's name is Charlie. In Stargate (1994), there is a certificate giving his name as Tyler.
When the crew first arrives at the crystal field, Sam identifies them as "granite, not volcanic." Yet granite is a rock made of many components, including various forms of crystals, but cannot itself form large crystals. Further, granite is an igneous rock, and thus always "volcanic." Later, back in the compound, she correctly identifies it as a quartz crystal.
Sara's letters to Jack list a Winter Park, CO address but a Denver area code (80310). Denver makes much more sense, both as a place a middle class family would live year-round, and as a reasonable distance for the "O'Neill" duplicate to travel from Colorado Springs in the course of part of a day.
When "duplicate O'Neill" first finds his locker, there is one to the left of it, that seems to be labeled "Feretti." Yet, when O'Neill opens the locker and the camera pulls back, his locker is on the corner with no other locker to the left.
The alien, as Jack O'Neill, visits the room of Jack's dead son at his ex-wife's house in Colorado. On the wall is a poppy pin, used by Canadians and most of the British Commonwealth to mark November 11 - Remembrance Day. While the US also uses November 11 to mark those who died in war - Veteran's Day - poppy pins are not used. An American boy would not own a poppy pin.
When O'Neill returns through the gate, General Hammond says they don't know who it is, although the person has the codes from the handheld device and so is being let through. But certainly SG-1 had its own unique code for the mission, and perhaps each person also had a unique code, allowing the gate controllers to know who is sending the signal. It also would likely be procedure for old codes to be blocked out, and O'Neill not be allowed through, at least until they could try to communicate via radio. The duplicate took some of O'Neill's things but he still wore his radio when he came through the gate.
Sam tells Teal'c she could tell a Goa'uld energy weapon destroyed the crystals because a melted edge "looked like the walls of the gate room after Apophis's guards shot up the place." Yet Teal'c WAS one of Apophis's guards who shot up the gate room, referring to the pilot's opening scene. Sam acts like she doesn't know this, and perhaps she doesn't, as Teal'c may not have shared this fact, but he was debriefed thoroughly when he came to Earth and his morals go against holding back that sort of information.