FAQ: The bundle is invalid. The key CFBundleVersion in the info.plist must contain a higher version than that of the previously uploaded version.
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When trying to upload a new updated binary to iTunes Connect via Application Uploader, many people are getting this error message even though they have updated CFBundleVersion in their info.plist file to a higher value. Some have even already successfully submitted different apps updates using the same method, but for whatever reason some particular app won't work upload.
The solution is quite simple.
You may have assumed that your Bundle Version for iTunesConnect purposes is the Version that everyone can see in the AppStore and you can see in "Version Information".
We also thought so, but surprisingly enough Apple use different data for theses purposes and you can find this info under: ITunes Connect > Manage Your Applications > Application X (your application in question) > View Details (bottom left corner) > Binary Details.
For some reason, despite having Version I in the AppStore and info.plist, the Bundle Version in for our app was 2.0. All we had to do, was update the new version to 2.0.1 and it worked.
Hope it helps.