Non-public API usage
I had this exact issue using Yosemite with Xcode 6.1 and using Objective C. I also got a warning on validation saying you can't upload an app created with a beta version of Xcode, which 6.1 is at the time of writing this.
I trashed Xcode 6.1 by dragging it to the trash form Finder then downloaded Xcode 6.0.1 GM from the App Store. I tried twice to install 6.0.1 over the top of 6.1 but it didn't work, hence the trashing of 6.1
Having cleaned and recompiled my app with Xcode 6.0.1 it validated and submitted to the app store with no problem. I hope this helps.
I fixed it by changing the deployment target from iOS4.3 to iOS5.0 all fixed using Xcode 6.1
I encountered the exact same error when using Xcode 6.1 (and its bundled Application Loader) on Mac OS 10.9.5. Clicking "Back" within the Application Loader and re-submitting the same binary worked. In other words, trying a second time succeeded. My app was built with iOS SDK 8.1.