If Japanese did not use kanji, there would be no confusion, I think. Not all characters are written the same, but a lot are. Some compounds have their elements reversed. But, as far as languages go, they are completely different in almost every way. Chinese simplifications don't always match Japanese ones and the accepted forms are also different in some characters.

Maybe Korean used to have this problem as well when hanja were regularly used, and it is very grammatically similar to Japanese. Though, at one point, both Japanese and Korean used classical Chinese as a writing system before adapting it to their own languages.

Chinese is also not just one language (despite what the government may like to think) as several of the "dialects" aren't even mutually intelligible. However, thy do all share a written language today. (I think Cantonese also sometimes writes things colloquially which is not the same as the standard written language).

As for other confusions, I'm not sure if MSA would work since it's shared by multiple different versions of Arabic that also may or may not be very similar.