I wasted many hours trying to fix this error:

It turns out that I had placed the Run Script phase above my Embed Frameworks phase in my watchOS target. It's a silly mistake, but it's easy enough to make and potentially annoying to debug. (Applications... require an iOS Development Target of 3.0 or later really? )
I think it would be useful to warn developers about this. I suggest an addition like this to the docs (my contribution is the section in yellow):

I would submit a PR, but I think the docs might not be on GitHub?
Tagging so devs can find this solution in the future.
ITMS-90081: This bundle is invalid. Applications built for more than one architecture require an iOS Deployment Target of 3.0 or later.ITMS-90209: Invalid Segment Alignment. The app binary at __ does not have proper segment alignment. Try rebuilding the app with the latest Xcode version.ITMS-90125: The binary is invalid. The encryption info in the LC_ENCRYPTION_INFO load command is either missing or invalid, or the binary is already encrypted. This binary does not seem to have been built with Apple's linker.Thanks for the suggestion, I updated our installation steps to emphasize this. It should be live in a few minutes.
Great! :smile:
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Tagging so devs can find this solution in the future.
ITMS-90081: This bundle is invalid. Applications built for more than one architecture require an iOS Deployment Target of 3.0 or later.ITMS-90209: Invalid Segment Alignment. The app binary at __ does not have proper segment alignment. Try rebuilding the app with the latest Xcode version.ITMS-90125: The binary is invalid. The encryption info in the LC_ENCRYPTION_INFO load command is either missing or invalid, or the binary is already encrypted. This binary does not seem to have been built with Apple's linker.