This always confused me, even as a native speaker so I looked it up some. Ultimately it’s because modern German is the confluence of multiple older, historic languages one of which came from a tree with a strict male/female rule for nouns while the other one’s grammar defaulted to a neutral case.
As languages merge or adopt from others they often becomes a conjoined mess of multiple rules coexisting at the same time. A contemporary example is that in English the plural of a word is usually formed by attaching the suffix “s” to the singular form, aka house becomes houses. However there’s plenty of exceptions (mouse, mice) in particular if the words stem from a different language (octopus, octopi but nowadays octotuses is also acceptable). In that sense to people not privy to the etymology of words and who only study/learn the language per se there would be no perfectly accurate mechanism to predict the plural of a word.