Does a Vietnam visa get rejected from Japan?
Yes. However, the chances are slim. Your Vietnam visa application will be denied only if your name appears on the Immigration Department's blacklist. If you have a good immigration history in Vietnam, you are not at risk. The Immigration Department has no reason to reject your visa application.
On the other hand, even if you have a valid Vietnam visa, the airline staff will not allow you to enter if you do not have a national passport valid for at least six months and a Vietnam e-Visa. It is recommended that you print your Vietnam e-Visa before traveling to the international airport. Please make sure your passport is valid for at least 6 months after your arrival in Vietnam.