With Xcode 4 came the concept of a workspace that allows multiple projects to be grouped together. Each workspace gets a unique set of symbol indexes, build products, window layouts, etc., otherwise referred to by Xcode as derived data. Since a single project can belong to more than one workspace this derived data is not contained under the individual project directory. This post explains how you could clean derived data.
Option 1: Delete the containing folder using Finder/Terminal
By default Xcode stores this data for all projects in a single shared folder under your home directory at the following location:
Option 2: Delete using Xcode
Open Xcode. Go to Window > Projects
Select the project from the list to your left to delete its derived data. Notice that this is the same place you have to come to restore/delete snapshots you made as well.