Jonathan suggest here: Xcode Includes .xib files that have been deleted! that cleaning all targets and empty the caches will fix the problem with Xcode including deleted .xi
Here's my shell script solution, which deletes derived data and cleans a project's cached assets, for Xcode 4, 5 and 6.
Sometimes, simply calling rm -rf on the Derived Data directory leaves a lingering file or two, but my script loops until all files are deleted.