Yesterday I was sent one from a partner saying that some files we were to transfer to their FTP server (yeah, I know it's 2017) were missing. So I logged into the server manually and checked -- the files were there, created at 5 AM, just like they are everyday when the cron job that generates them was run. So I started my response by saying, "I just checked the server manually and the files were there. Why do you consider them missing?"
But then I started to think...would this reply come off as if I were questioning their intelligence? They must believe that the files actually aren't there, or else they wouldn't have sent me an e-mail asking. The same process has been running everyday since February of last year, however, and presumably they had never failed to find the files before yesterday.
I just sent the e-mail anyway, but it is interesting that I've been conditioned to question myself over a very innocuous reply to make sure my tone was appropriate, as to not risk offending the other party.