We ran into the same issue, and just found a workaround.
So in most of the cases, the header is located at MyFramework.xcframework/ios-arm64armv7armv7s/Headers/MyHeader.h. If your project includes another xcframework also containing MyHeader.h, you will get this copy header error.
The workaround is putting all the headers in a subfolder, for instance we can move the header to MyFramework.xcframework/ios-arm64armv7armv7s/Headers/*my*/MyHeader.h and AnotherFramework.xcframework/ios-arm64armv7armv7s/Headers/*another*/MyHeader.h, then during the build process there will no conflict any more.