@Nenin: I see a similar popup sometimes. If I remember correctly, It is when I have a workspace with at least 2 projects and the selected Target is from project A but the currently selected project is B ****.
This is possible, I tried to refactor old soft which also use a dozen of the small custom libs. I faced such glitch for the first time and was brutally surprised.
You have a Xcode workspace containing two or more separate projects.