Knockaert had been in all 17 matchday squads so far this season and rumours had been circulating pre-match that the winger was set to miss out, despite being at the John Smith's Stadium.
That proved to be correct as the French player was not included in the squad and Hughton said afterwards: "I made a decision that the way they play, with their full-backs very high and wide and I felt we needed to be very compact today.
"In our normal game and the way we play with two out-and-out wingers, there are lots of positives from it, but it can also leave you open particularly away from home and against a really expansive team.
"I just wanted to be a little bit compact, certainly the team formation did not have anything to do with the two goals we conceded.
"Anthony was here, it was just a decision to leave him out, he has played a lot of games and is a high intensity player. We have a squad at the moment that is very competitive and pushing and we are going to have to use them over a lot of hard games."
On the result, Hughton added: "I am incredibly disappointed these are a good side, very good side at home. If you afford them the two goals we did, it becomes very difficult to come back from that.
"In this division, particularly away from home, you have to play at a level to be able to come back from that. We never allowed ourselves to get into the rhythm that we needed to. Certainly the better team won and the two goals, particularly the first, were disappointing."