Kovid is
currently working on various bits and pieces of basic EPUB3 (metadata) support. See the Changelog for v2.59 which included some EPUB3 Nav support, and various
I doubt it is deliberate, whatever the problem is.
I don't do EPUB3 so I can't test it... but do you see the same problem when you checkout the v2.59.0 release tag? Or did this occur in between v2.59.0 and HEAD?