Hi Theo,

We encountered something similar when we migrated a site. We properly redirected all the old url's to the new one, however, in the weeks after the migration, we saw a huge increase of 404 in the webmastertools.

When we took a closer look to these url's, we noticed that these where using an url structure we had abandoned several years ago. On the "old" site, these were redirected, but we didn't implement these old redirections after migration as we assumed that these very old url's wouldn't be in the index anymore. We proved wrong. We could delete them manually from the index using webmaster tools, because they used folders we are not using any longer, this is not probably not possible in your case.

While it is a bit annoying, I don't think that having these "phantom" url's in the index is doing you any harm in terms of SEO. They will probably never pop-up for normal search queries, only when you do in-depth queries, limiting the results to only your site.