"Invalid Swift Support - The SwiftSupport folder is missing" with Xcode 7.3.1
The solution here was in this answer. We needed to use the new -exportOptionsPlist flag with xcodebuild instead of the older -exportFormat and -exportWithOriginalSigningIdentity flags. The plist just needs to have the method key set to app-store.
The root cause of this is that the provisioning profile is ad-hoc and it doesn't create SwiftSupport directory in the ipa. The folder is created using app-store as the export method, so it worked for me when I updated my provisioning profile to app-store.
In my case, I just added redundant swift file to the project and it solved the problem.