A lot of countries including Japan have visa-free entry for tourists. But being permitted to work without a visa is much rarer (although it does happen e.g. in the EU).
A visa in Japan is almost always legally under the individual's control/responsibility (and this is generally a good thing, as it prevents companies using the visa to control their employees). The company can pay a lawyer to do your application but it's still the individual's application and the individual's responsibility legally, if they e.g. submit false info about what kind of work they're going to be doing then it's the individual who'll be held responsible.
Honestly I'm struggling to think what the company could have done to screw the application up - if they e.g. failed to remind her to renew her visa before it expired then that's still her responsibility legally and (IMO) morally, if they failed to supply required documents then correct procedure is to submit the application without them with an explanatory letter saying the company was fucking around (and then in theory the MOJ should bollock them, although in practice who cares about screwing over foreigners). Obviously if the company told her they'd take care of it and didn't then that's kind of morally their responsibility, but in a way they were lying from the first if that's what they said - a company can help you with your visa application but they can't ever take full responsibility for it, it's going to be in your name and if you don't take the time to understand the relevant laws and your responsibilities then you're putting yourself at risk.
