There are many, heaven knows, but one of the biggest is the non-answer. That is, the degree to which a query is sent to an editor but receives no acknowledgement, leaving the poor writer wondering whether the message got through at all.
One can argue that these days one employee at the destination is trying to replace two downsized colleagues and has no time to respond to all the incoming e-mail. That argument may have a basis in fact and might explain a delay but it doesn’t excuse the plain rudeness of leaving people in limbo forever.
It’s doubly discourteous when the writer is politely waiting to hear whether you want the story or not. After all, he or she is offering you something of value–if not to you, then perhaps to another publication and most definitely to the writer.
Meanwhile, given that we’re all computerized these days, it seems to me the technological tools available make the “lost in cyberspace” issue unnecessary. It would not be that hard to set up a “We have received your query and will get back to you within X days” message template and another for “Thank you for your query but we cannot use your story at this time.” A quick copy-paste (or mail merge if there are many queries per day) would free the writer to query elsewhere, and clear the editorial conscience of the nagging feeling one has been unkind. It would probably be even easier to have queries submitted via a web-form so that those responses could be automated.