This seems to be a long-standing Ubuntu problem, I've experienced it since years ago if I remember correctly.
I have language support for both Chinese and Japanese installed (and want to keep it that way -- I do know though that the problem can be "resolved" by uninstalling Chinese fonts, I have experimented with that). The problem is that Japanese text shows as Chinese glyphs. Not for every single Japanese character, but presumably for ones that the system thinks has a corresponding glyph in Chinese.
This happens in all applications: libreoffice, browsers, gedit, terminal etc.
(This problem is not about input methods.)
Fonts installed:
Chinese (and Japanese)
fonts-arphic-ukai
font-arphic-uming
ttf-wqy-microhei
ttf-wqy-zenhei
Japanese
fonts-takao-gothic
fonts-takao-mincho
fonts-takao-pgothic
Others that seem to support Japanese/Chinese
fonts-droid
Steps to reproduce: Install fonts/support for both Japanese and Chinese, and then type Japanese character. You need to be able to recognize differences between glyphs from the two languages to see this problem.
Examples: 誤り、直す
(Will upload pictures.)