I have had the same issue with my native application.
I am using Carthage (https://github.com/Carthage/Carthage v.0.15.2) where I have a dependency D1 which have a nested dependency D2.
I'm not exactly sure what went wrong, but when archiving these dependencies it happened that a dSYM file from D2 sneaked into the archive in the framework folder of D1.
I deleted the dSYM file from the archive, and I was able to submit.
So please take a look at your archive and see if there are any .bundle, .dSYM or the like, a place where it shouldn't be.
This is where I found the source of my troubles:
~/Library/Developer/Xcode/Archives/2016-04-14/ARCHIVENAME.xcarchive/Products/Applications/APPNAME.app/Frameworks/D1.framework
This issue might be caused by either Carthage or the frameworks, or something completely different, so the above mentioned "solution" is a workaround for now.