Smith was unhappy with referee Craig Charleston for red-carding defender Craig McKeown and also awarding Raith a free-kick immediately before their last-gasp winner.
“I have a lot of respect for John McGlynn,” he said. “It wasn’t his team I was having a go at. I was unhappy with the officials, and that’s what I was talking about.
“I am disappointed John felt the need to come out and say what he has, but as far as I am concerned it is finished.”
Smith faces a defensive headache for Sunday’s game against Stirling, with McKeown, Rhys Weston and Gary Irvine all suspended, leaving only young Kyle Benedictus as the only recognised centre-half.