Update MANIFEST.SKIP to exclude MYMETA files. If you are lazy, add "#!install_default" in your MANIFEST.SKIP and update your ExtUtils::Manifest if necessary, then some of the most common files will be excluded.
Upgrade the bundled version of Module::Install to the most current release. Alternatively, you can switch to another build system / installer that does not suffer from this problem. (ExtUtils::MakeMaker, Module::Build both of which have their own set of problems.)
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
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.