Mackay-Steven was clean through on Hoops goalkeeper Lukasz Zaluska after playing a one-two with Johnny Russell but his shot slipped past the far post.
Celtic made him pay as two goals from Gary Hooper and one apiece from Victor Wanyama and Scott Brown secured a comfortable victory.
Houston said: "Who knows what would have happened had we scored? But when you come here you always want to take the chances you create and if we score first it puts them on the back foot.
"But even at 2-0 at half-time I said the next goal was all-important and I felt that Celtic were getting a wee bit edgy at times.
"If we get that next goal we are back in the game but they got the third goal and the game is over and done by then."