I am also having the same issue. I've been at it for three days, trying to submit to iTunesConnect for a TestFlight distribution but getting rejected for an invalid binary every time. I am using Yosemite and XCode 7.0.1. I tried revoking all certificates and profisioning profiles, deleting those certificates and profiles from my Keychain, then generating new certificates and profiles, downloading them and signing with those, but nothing worked. I also deleted the build folder, and cleaned the project like the email told me to.
Dear developer,
We have discovered one or more issues with your recent delivery for "MyApp". To process your delivery, the following issues must be corrected:
Invalid Signature - The binary with bundle identifier 'com.mycompany.myframework at path [myframework.framework] contains an invalid signature. Make sure you have signed your application with a distribution certificate, not an ad hoc certificate or a development certificate. Verify that the code signing settings in Xcode are correct at the target level (which override any values at the project level). If you are certain your code signing settings are correct, choose "Clean All" in Xcode, delete the "build" directory in the Finder, and rebuild your release target.
Once these issues have been corrected, you can then redeliver the corrected binary.
Regards,
The App Store team