The Jenkins Xcode plugin builds the IPA file by invoking this command:
/usr/bin/xcrun -sdk iphoneos PackageApplication -v <pathToAppDir> -o <pathToIPA> --embed <mobileprovision> --sign <signingIdentity>

Xcode7's "PackageApplication" perl script invokes the "codesign" command to sign the built IPA, which includes the ResourcesRules.plist file and signing the IPA with this piece of metadata. This results in iTunes Connect rejecting the IPA during submission.

See the following links for more details and possible solutions/workarounds:
http://stackoverflow.com/questions/32504355/error-itms-90339-this-bundle-is-invalid-the-info-plist-contains-an-invalid-ke
http://stackoverflow.com/questions/32763288/ios-builds-ipa-creation-no-longer-works-from-the-command-line/32845990#32845990
http://cutting.io/posts/packaging-ios-apps-from-the-command-line/