When replying a GitHub mail, I usually do inline quoting.

Only recently I realised that lines starting with ">", the common quote character, will not show in issue comments. Thus replies created by emails may get a very different meaning.
Compare what is shown:

with the real content shown after clicking "edit":

Either GitHub should show both quote and answer or suppress any quoting to avoid confusion.
If quoting is not desired GitHub should state so in its emal notifications.