I have the same issue for Xcode beta 3. My use case is
A(Swift Package) -> B (Binary)
For the first time I open A package, the compiling is fine. But after I run a build clean, then it pops error 'Module B is not found'
I also tested the following use case.
A(Xcode project) -> B(Swift Binary package)
It worked well.
CoretTIAN
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This is fixed in Xcode Beta 3