Xcode warning: "Multiple build commands for output file"

In the Project Navigator, select your Xcode Project file. This will show you the project settings as well as the targets in the project. Look in the "Copy Bundle Resources" Build Phase. You should find the offending files in that list twice. Delete the duplicate reference.

Xcode is complaining that you are trying to bundle the same file with your application two times.

This is easily caused when you add git based subprojects. Xcode isn't smart enough to ignore the .git subfolder even though you can't see it from finder, so it will get very confused that there are multiple files named "master" or "exclude", (standard git repo files). With Xcode4, go to the project (root of the left tree) then click your app target and expand "Copy Bundle Resources", then remove all the references to .git, you shouldn't need them baked into your app anyway.

Actually, the answer to this is quite simple.

In your Xcode project search for the files which raise the warning, and just delete one of them.

Xcode will show only one reference of that file in the search results, but don't stop there, go ahead and delete it. (it's better to make a backup of your project file before deleting it)

Now build the project again. The warning should disappear now.(this answer is for a previous version of xcode)