I think you can get an error like this when building if your project was modified by Xcode 5 and you went back to Xcode 4.6 and tried to build, because Xcode 5 can remove some things that will cause unexpected results on Xcode 4.6. But it sounds like this mainly applies to OS X projects and not iOS ones, so I'm confused as to why this would happen for iOS. I would suggest trying to build your project with Xcode 5 to see if that resolves the issue.
If you take a look at this, you can see a long explanation for the reason that this happens. But basically Xcode 5 has a different "default" for some compiler settings than Xcode 4.6, and Xcode 5 recommends removing certain settings sometimes because of this, which makes Xcode 4.6 behave differently.
A good solution, since it sounds like something might have gotten messed up with your project (since it's showing options for OS X for a supposedly iOS project), is to create a new project and move your files over. If your project is under source control and you don't want to scrap your current repository and revision history, you could always create a new project and compare the project files to see what differs between it and a clean Xcode 4.6 project.