I'm not in this space, but the similarity in names made me wonder if these would really have started around the same time, with an unclear "dependency order", so I reached for a search engine, and according to Wikipedia, CPAN (1993) is based on CTAN (1992).
There isn't "some question", there is a definite answer, namely in "Programming Perl" and I quote the 4th edition, page 629:
History
Toward the end of 1993, Tim Bunce, Jarkko Hietaniemi, and Andreas König set up the perl-packrats mailing list to discuss the idea of an archive for all the Perl 4 stuff floating around the Internet. Perl 5 development had started that year, and one of its main features would be an extensible module system that would allow people to extend the language without changing perl. Jared Rhine suggested he idea of a central repository, but nothing much happened. His idea had come from CTAN (http://www.ctan.org), the Comprehensive TeX Archive Network.
Edit: fix markup
I may not completely understand what you're describing, but with perlbrew managing different Perl versions, and various CPAN clients installing modules in versioned libraries - as well as the test/smoke servers that test CPAN on tons of versions of Perl for Perl CPAN authors automatically, I don't know if I've come across what you're describing.
What's still a pita is when there's an outside dependency from the Perl ecosystem that breaks a module, but I'm not sure that's Perl's fault.