In a one-sided second-half, Joe Ledley, Georgios Samaras and Anthony Stokes racked up an unbeatable lead before Hoops skipper Scott Brown scored from the spot a minute from time after Samaras was fouled by Sean Dillon.
Houston, who believes Neilson did not have to make the challenge, said: "It's hard enough trying to beat the champions-elect with 11 players never mind 10.
"I haven't seen it yet but what I would say is that Robbie is on a yellow card and it's a challenge that he makes inside Celtic's half. I can understand if it was around the penalty box and they were going to score.
"He is not a dirty player but he is an experienced enough guy, he should back off and not go into a challenge like that.
"It was a pivotal moment because effectively, it had a bearing on the game, rather than us being able to continue that good start we had, we had to take off a young flair player in Gary Mackay-Steven."