Recent WP may have caused the install hundreds of po and mo files in one place

Yesterday I installed a new plugin into my Multisite/Network. This is the first plugin install since updating to 4.5 and I think the choice of plugin (Advanced Custom Fields PRO) is probably irrelevant.

After the plugin finished installing there was a further 30 minute update where WordPress said “Oh and I’ll just update the Bulgarian locale for askimet”, “Oh and I’ll just update the Bosnian language locale for askimet”, …, …, “Oh and I’ll just update the Chinese language locale for askimet”, …, “Oh and now I feel like updating the locales for bbpress”, … “Oh and while I’m at it I’ll update the locales for captcha”, “contact-form-7”, …, …, “wordpress-importer”.

This process installed some 286 files in the wp-content/plugins directory totalling 15 MB.

Then WordPress said “I’m going to do the same for all the themes you have installed”, resulting in a further 750 files in wp-content/themes 8 MB.

My question is:
Has someone accidentally tried to use ‘-‘ as a directory separator; have I got some configuration variable unset; or is it genuinely the case that all language files now go in the top level of these two directories as flat files?

If not, where do these files really belong? How might I clean up the mess? And what’s to stop WP noticing that the files are not there and pulling them in again?

Thanks
M