I recall after 9-11 there was a spike in hatecrime against anyone who looked even vaguely middle eastern or Muslim, such as Sikhs, Hindu, etc.
I assume it could only have been much worse in an era with more limited exposure via media and education, but I've never actually seen anything on the subject.
The answer to that is a firm yes. There were numerous cases of "mistaken identity" all throughout the war. Personally though, I feel images speak louder than words.
US Army Leaflet on how to tell the difference between a Japanese and Chinese
You also might be interested in the 1982 case of Vincent Chin, a Chinese-American man mistakenly murdered by a pair of disgruntled anti-Japanese auto workers.
In addition to what the other people have said, there are arguments that can be made that during the war, Chinese Americans experienced some gains (think in terms of business and such) from anti-Japanese fervor at the expense of Japanese Americans.
