When you reply to a message in Outlook 2010 or earlier, Outlook creates a new message in a free-floating window. When you hit Reply (or Reply to All) in Outlook 2013, your reply appears "inline," above the original message in the viewing pane on the right this works well on a touch screen tablet but on a normal desktop PC not so much.
Many of the message options available in Outlook 2010 aren't available in Outlook 2013, and it's easy to lose track of your reply when switching to other apps, unless you click Pop Out at the top. Pop Out makes Outlook revert to the 2010 behavior.
Solution: In Outlook 2013 Click File, Options, Mail. In the Replies and Forwards section, check the box marked "Open replies and forwards in a new window."