Loki's scepter contains the Mind Stone, not the Space Stone. This is what gave it the power to control other people's minds. In Avengers: Age of Ultron, the Mind Stone is used to help create Ultron, and is later removed from the sceptre and implanted in Vision's body.
The Tesseract - which, as you said, does contain the Space Stone - is a completely separate artifact. The two objects were also present simultaneously in the original timeline: recall the scene at the beginning of the first Avengers film in which Loki steals the Tesseract while using the scepter to brainwash Erik Selvig and Hawkeye. This would have been impossible if, as you claim, they're the same thing.
Your confusion is no doubt due to the fact that the sceptre's light is inexplicably blue, even though the Mind Stone is yellow.