In SyFy's oral history of "Stargate SG-1," Robert C. Cooper detailed another adjustment that he and the writers had to make after the Air Force objected to a specific line. This particular issue arose from the show's inclusion of the real-life military base at Area 51. Everybody knows that infamous location's reputation, but it seems the Air Force was keen not to encourage any extra-terrestrial associations.
In the world of "Stargate," which includes all the movies and TV shows, Area 51 is a secret Air Force base that's home to a research facility for the Stargate program. In a season 2 episode of "SG-1," entitled "Touchstone," the crew suspects the National Intelligence Department is using Earth's second Stargate, which is stored in Area 51, prompting Jack O'Neill and Teal'c (Christopher Judge) to pay the site a visit. When they arrive, they're greeted by Air Force Major Albert Reynolds (Eric Breker). O'Neill then asks the Major, "Is this where you're keeping the little green men?" But it seems the real Air Force wasn't all that fond of the line.
As Cooper explained, the Air Force called the writers and said, "There are no aliens at Area 51." Cooper continued, "We said, 'We're not saying there are. Jack is just asking a question," But that wasn't good enough. Series co-creator and executive producer Jonathan Glassner added, "They said, 'there are no aliens at Area 51, period.' We said okay, it was a joke, so I went back to them the next day and said, 'how about if Jack says present company excluded, talking about Teal'c, and accepts that there are no little green men there?' and they said that's fine."
This is how the interaction plays out in the actual episode, with Reynolds saying explicitly, "There are no alien life forms at Area 51," before O'Neill replies, "Present company excluded, of course." While the writers satisfied themselves and the Air Force by including these lines, it does seem a bit odd that the Air Force would deny the existence of aliens at Area 51 to a man whose job is to travel to alien worlds and another who is a literal alien. But at least "SG-1" didn't get on the bad side of the U.S. military.