The following warning, ‘Multiple Build Commands For Output File’ occurs when you try to delete resource files by ‘delete reference’ other than the correct method of‘move to trash’ while deleting files from ‘Resources’ folder of your project. Therefore the Copy Bundle Resources still holds the references of the same file you have deleted and it shows the multiple build commands for the output file after you added the same files over again.
How to Fix? :
Go to the Targets->YourProject->Copy Bundle Resources
From ‘Copy Bundle Resources’ delete those files whose reference are still there or files which shows the warning.
Here ‘YourProject’ is your project name.