(at around 45 mins) When Jackson gets out of the cab, his leg appears to have been amputated above the knee. Later, when his prosthetic leg is shown, it seems to be designed for someone whose leg has been amputated below the knee. Further confusing matters, when he walks into the bookstore both legs bend at the knee, despite the fact that his left leg seems to have neither a knee nor an artificial knee joint.
Samantha Carter has the rank of Lieutenant Colonel; however the character is already a Colonel, promoted in the fourth season of Stargate: Atlantis (2004). In Search and Rescue (2008), the events of this film are confirmed to have happened after Atlantis's fourth season.
When Ba'al kills Apophis, he orders his slaves to clean up the mess, but no one does so, nor does Teal'c or any of the Jaffa order anyone to do it. Furthermore, the girl with the towel walks through where the mess should be, but obviously isn't.
(at around 1h 16 mins) Carter reports 6 bogeys per her F-15's HUD that turn out to be Russian MiGs, but only 5 MiGs fly past to engage the pursuing death gliders.
(at around 1h 13 mins) When Mitchell gives the order to break right after the KC-135 is destroyed, the hose to his oxygen mask is attached to the right side of his mask. In all other shots, his hose and those of Carter, Jackson, and the other pilots are attached to the left side.
(at around 1 min) When Major Davis is seen at the beginning of the film he is wearing blue rank slides and not metal rank insignia on his jacket.
(at around 50 mins) Dr. Jackson's prosthetic leg seems to have a clear plastic "fitting" socket. These sockets are used only to ensure that the final socket (made from carbon graphite, or more rarely fiberglass) fit properly. Fitting sockets are not durable enough for daily use.
(at around 1h 19 mins) The AK Cameron receives from the Russian soldier is Chinese, not Russian, and has a hooded front sight, smooth dust cover and bolt carrier "in the white". A Russian AK has an open front sight, ribbed dust cover and painted bolt carrier, and no Russian soldier would have a Chinese firearm.
When Mitchell is being formally briefed about his future conduct, he is told to have no contact with "Mr Jackson or Miss Carter". The officer should have used their titles, 'Doctor' and 'Colonel' (or 'Lt Colonel'), which they had in both timelines.
(at around 28 mins) While Carter and Mitchell are walking through the Arctic, a helicopter can be seen flying over one of the hills in the background as the shot fades to the next sequence. However, since the US military is conducting a training exercise in the area at that time (as Jack confirms later), there is no error in having a helicopter flying around.
(at around 35 mins) On the submarine, Jackson says Jack is from Minnesota. During the series he is from Chicago. The character was born in Chicago but raised in Minnesota. So both statements are correct, depending on context.
(at around 1h) The F15s SG1 take to Antarctica are described as having "minimum armaments and extra fuel tanks" and that is how they are configured on the runway In the refueling scene though they have missiles loaded and not fuel pods. The other in-flight shots have a variety of different configurations probably because stock footage was used.
(at around 1h 6 mins) Ba'al's hand doesn't actually press any buttons to hang up the phone on President Hayes, a sound effect is heard but his fingers are nowhere near any buttons on the phone.
(at around 48 mins) When Samantha Carter is at the Grocery Store, she picks up a box of "Frootees". However, on the side of the box you can see the "Kellogg's Rice Krispies" logo.
At around halfway through the movie, when Carter is about load the grocery she shopped into her and the Alkesh ship flies through town, the camera pans over the side of the car. A sticker with a barcode can be seen in the rear side window, indicating this is a rental car rented by the production company.
(at around 1h 30 mins) In the Closing Credits, Qetesh and Qetesh's Jaffa are misspelled as Quetesh and Quetesh's Jaffa.
(at around 1h 29 mins) When Cameron waits for Ba'al on the ship, he has two Thompson submachine guns. The one he gives to the crew member, the M1 Thompson, was not developed until after 1939 during WWII. They should have been 1921 or 1928 Thompsons.
(at around 27 mins) While Carter and Mitchell are walking through the Arctic they are supposed to be traveling south to get into radio range to call for help. As they are walking the sun is seen behind them. North of the Arctic Circle, walking south the sun would only be behind you when it is the midnight sun. An earlier scene, though, was at night and Mitchell said he saw stars. That means there would be no midnight sun and the sun would not be above the horizon unless well away from north.
(at around 5 mins) In the beginning, when Vala (and all the others) disappear, the team still remembers her like she was still there. If the timeline did change, the team would have no knowledge of her (and anyone else) because they would never have met. Likewise, circumstances would change and they would never meet on the planet to extract Ba'al.
When Cam Mitchell visits the farm he visited as a child, the current owner is clearly not a relative, since Cam is a grandfather paradox because his grandfather died before marrying and procreating. Therefore there is no logical reason for the farmer to keep a portrait of Mitchell's grandfather on his mantel when the man was no relation.
The initial premise is that it is impossible to distinguish Ba'al from his many clones. However, the original host is presumably the only who carries the Ba'al symbiote. It should have been easy to tell if the 'Ba'al' in captivity has a symbiote.
(at around 1h 30 mins) Don S. Davis is credited as Major General George Hammond; however, he clearly has three stars on his uniform, which would make him a Lieutenant General. Hammond was a Major General in seasons 1-7 of Stargate SG-1 (1997) and later promoted to Lieutenant General when the character dropped to recurring status in the later seasons.