The MIS-communication of email

Have you ever gotten a response to an email where you end up sitting there, scratching your head, going "WTF just happened here?" I got one of those yesterday and as I was reading it, I was thinking "There is no way that what I said could have been taken that way." Hmm.....I don't know. And the response I got doesn't even merit a response in turn, however, I am one of those people who feel like my silence will mistakenly portray that there response is accuarate; what's a girl to do?