This is also happening to me and is preventing me from deploying to Itunes. I get a Transporter Error:
[04:36:09]: [Transporter Error Output]: ERROR ITMS-90680: "Invalid directory. The bundle Payload/BinarySPMTest.app/PlugIns/Binary.framework is not contained in a correctly named directory. It should be under "Frameworks"."
[04:36:09]: [Transporter Error Output]: ERROR ITMS-90685: "CFBundleIdentifier Collision. There is more than one bundle with the CFBundleIdentifier value 'com.test.binary' under the iOS application 'Test.app'."
[04:36:09]: [Transporter Warning Output]: WARNING ITMS-90806: "CFBundleIdentifier collision. Each bundle must have a unique bundle identifier. The bundle identifier 'com.test.binary' is used in the bundles '[Payload/BinarySPMTest.app/Frameworks/Binary.framework, Payload/BinarySPMTest.app/PlugIns/Binary.framework]'"
[04:36:10]: Transporter transfer failed.