Clark was convinced that Blues had a legitimate first half goal ruled offside when he thought the goal should have been allowed.
Just past the half-hour mark and with Blues trailing 1-0, Clayton Donaldson appeared to touch Koby Arthur's shot into the net but the referee's assistant raised his flag for offside against Donaldson and the goal was disallowed.
"After the first goal there was only one team in it and we had a legitimate goal taken off," the Blues boss said after the game at The Valley.
" I've seen the footage and it's not offside. I've spoken to the ref but I can't take the actual footage in.
"The defender, who is going out with Paul Caddis, he actually ends up over the line with part of his body so he is playing Clayton Donaldson on. Then the goalkeeper is also playing Clayton Donaldson on.
"It's a goal. It doesn't matter who touched it, he's not offside. I have seen it three or four times and it's another major decision that's gone against us.
"We drew 2-2 at Norwich recently and I was told we should have had a penalty plus their lad given a straight red card. And on other occasions this season we have had goals chalked off etcetera."