Fix MANIFEST.SKIP or use an authoring tool which respects MANIFEST.SKIP. Note that each entry in MANIFEST.SKIP is a regular expression. You may need to add appropriate meta characters not to ignore necessary stuff.
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.