Depending on what is said, in most cases “freedom of speech” doesn’t include the right to slander or harass people. While the company didn’t elaborate on what was actually said, the examples that they don’t allow all include things that would normally not be protected by said freedom of speech laws, those acts being announcements of violent acts, threats, and intimidation
that being said, it shows the culture differences between Japan and where I live because I could never imagine a company directly assisting an employee with those types of cases here.