A similar thing happened to me.
I was using phonegap build for creating my .ipa file.
My Tip is to look at the path of the file mentioned in the error message.
When I looked at it it seemed to refer to a file that was not part of my project at all.
It turned out that my build process did not do a proper cleaning of the folder into which it copied the files to be zipped and sent to phonegap build - so that old files where still included.
Adding a proper cleanup initial step to my build proccess fixed the issue right away.
