I wish RPG maker had a "go back" option in dialog like Renpy does, but the brief window should help a bit. Usually it's because when seeing a scene that's a permutation, or copy of, of a previous one, I tend to skim a bit and don't always remember exactly which dialog comes before the prompt. So hopefully a second delay will let me see the option pop up.
Upon revisiting the dialog, I think one other thing that might help is having the input be after the guy says his dialog instead of after the PC says "... ... ..." as the longer dialog window I think helps prevent accidentally hitting the input. Usually the first thing I do when I see a dialog window is hit enter to see the entire dialog right away. But when the dialog is so short, sometimes it all shows up before I hit enter and the enter becomes an input instead.