Yea the open cascade kernel underpinning freecad (and python libraries like build123d and cadquery) has a number of rough edges. Many can be avoided, but that unfortunately requires a bit of experience.
IMO, lofts are often not the best tool for many jobs, but planning around fillet issues can be a pain.
I'd really like to use it and master it further, but CAD is not something I need often, and in F360 any geometry I've needed just works.