I am experiencing similar issue with xcode 12.4. I am working with a large project with many "version.h" files for example that I am not at liberty to change the names. The project was cleaned before building. What can I do to get it to work? Thank you.
Build system information
error: Multiple commands produce '/Users/..../build/Distribution-iphonesimulator/usr/local/include/Version.h':
Target 'vncviewersdk' (project 'vncviewersdk') has copy command from '/Users/..../common/libs/plat/Version.h' to '/Users/..../build/Distribution-iphonesimulator/usr/local/include/Version.h'
Target 'vncviewersdk' (project 'vncviewersdk') has copy command from '/Users/..../native/common/Version.h' to '/Users/.../build/Distribution-iphonesimulator/usr/local/include/Version.h'