I ran into the same problem today. It seems that iTunes Connect is recompiling apps with bitcode so that the UUID changes, and the dSYM inside the .xcarchive can't actually be used to symbolicate the app (this appears to be a new development).
You can download the correct dSYM from iTunes Connect. Login, go to My Apps, select your app, then tap on the Activity tab at the top. Tap on the relevant build, and, assuming the app was submitted with symbols in the first place, you should see the option to "Download dSYM."
The file you get is called dSYMs (without an extension) but it is in fact a zip file. Add the .zip extension, unzip, and you'll find your dSYM(s) inside.
You can upload this .zip file directly to Crashlytics and you should be all set.
The solution was posted here: https://twittercommunity.com/t/not-matching-uuid-bitcode/61000
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