I suffer from the occasional markdown glitches using branchable.
I've found that switching my own non-ikiwiki projects to https://github.com/jgm/CommonMark has helped sort them out for the most part.
ikiwiki does not implement Markdown on its own: it uses one of several third-party libraries, with the current recommendation being Discount. Out-of-process implementations like pandoc are not suitable to be the default for performance reasons.
There seems to be a Perl binding for libcmark at https://github.com/nwellnhof/perl-commonmark, but unfortunately its README points out that the libcmark API is not stable, which means libcmark and perl-commonmark would have to be upgraded in lockstep: this makes them awkward to deal with in Linux distributions. As a result I'm not going to look into this myself until there is a stable API for Commonmark available in Debian.