Deliberate mistake: According to the mission patches, both the Independence and Freedom are assigned the mission ID of STS-98 (possibly referencing the film's 1998 release date, and is around where the actual STS numbering was at the time). Two problems with this: First, they are two separate shuttle flights, so each should receive its own mission number. Second, STS was the coding for NASA's civilian shuttle. The shuttles in the film are Air Force vehicles and would probably not receive STS designations.
Deliberate mistake: Before the two shuttles dock to the MIR station, Lev initiates a rotation to simulate gravity. The shuttles then dock with their side hatch pointing to the anchorage. As the gravity is pointing away from the centre of revolution and the station is revolving around its main corridor, the gravity would push the astronauts back in to the shuttle and not towards the floor of the gangways leading to the shuttle or towards the floor of the shuttle. Also, the artificial gravity would be reduced to almost nothing at the main corridor. But here the artificial gravity somehow points down in every part of the station, and appears to work equally well throughout the station. (01:09:40)
Deliberate mistake: When the bomb is going to be remote detonated, on the inside lid of the briefcase, the remote destruct warning says that upon activation, the warhead will detonate in T minus 10 minutes. When the countdown begins on the bomb however, it is only for 6 minutes.
Answer: If you look at the deleted scenes on the special edition DVD, you will see a deleted scene in which A.J. asks what they needed a gun for, and Max explains that it's for debris elimination, in order to take out small rocks in the way.