The Toffees clinched all three points through a late header from Tim Cahill.
Hughes said: “Ideally we would have preferred three more points but we have games coming up where we need to start putting points on the board.
“We can’t dwell on it too much. We have got to get on with it with Christmas coming up.”
Hughes added: “To lose at the end is disappointing.
“We need to be better in those situations. We just switched off and they capitalised on that.
“I do not think either side did enough to deserve the victory. Everton got people behind the ball and managed to stop us playing our type of game.”