The loss puts them 21st in the table, only one point clear of the relegation zone, but Harris is buoyed.
"I'm disappointed for my players. I thought they were fantastic from the first minute to the last," he said.
"Everything that was asked of them they have done. I thought we were better than the best team in the league.
"I thought (the referee) got two decisions wrong for two goals. Looking back now, there are clearly two fouls.
"The Knockaert challenge on Lee Martin in the run-up to the third goal was clearly a foul, and the tackle on Shane Lowry (by Gary Taylor-Fletcher) in the run-up to the first goal, which was always going to be crucial, was a foul as well.
"Myself and Scott will keep going until we are told otherwise and the board find the right man.
"The biggest thing for me is that I want the players to play with a bit of freedom and show what good players they are. I don't feel pressure for me or the club, I feel it for them, because I want them to enjoy playing here."