Ok, imported e21-plain, used it as an SCE dep for emodule-alarm, and I see the same.
What has happened is that there is package listings in that enlightenment repo that don't exist, so they don't get merged. Our ability to use list files and create meta packages depends on package names being allowed to not exist, so to prevent them from not being listed would break a lot of the import features we know of. Until the numbering issue we see here we just never saw those the issue.
But I will take another look and see what we may can do to at least let folks know when a package name does not exist in a repo.