If my computer is offline or I've stepped away from it and I receive a message during that time, normally I would receive an email some period afterwards. Because I also have the HipChat app on my phone, I get notification about the message and even though I reply/read the message on my phone, I still get an email about the missed message.

It would be nice that there was some delay that would wait to see if a reply is issued through the phone app that it would not send the missed message email.