The Iron were beaten 3-0 at Crawley in the opening fixture of their League One campaign, but Knill felt a penalty was wrongly awarded against his side and a foul was missed prior to the third goal which killed off the game.
"Crawley’s second goal was never a penalty and everyone stopped in the build-up for the third when a blatant foul was made but the referee didn’t see it," he said.
“The referee’s performance was not too good at crucial moments and was a shocker. The second goal killed the game but it was not a penalty. If you don’t have the rub of the green it becomes difficult.
“At crucial times decisions went against us. We had created good chances but you have to take them and our finishing let us down.
"It was never a 3-0 game. It was disappointing that we had opportunities and, in that regard, the scoreline did not really reflect what happened in the game.”
Mark Duffy's red card with five minutes to play ended any faint hopes of a fightback, but Knill was content with Malone's decision to end the winger's game.
The second yellow card came for a foul, but he had been booked earlier in the match for dissent.
"It was a poor sending off and it puts us under a bit of pressure now to lose a player," he said.
Richie Barker, the Crawley boss, conceded his team could have conceded plenty of goals themselves in an open match.
“The players looked nervous at times but the performance was excellent in terms of chances created. In League One you won’t dominate games all the way through and this was a match where it could have been 6-3," he said.
“We need to keep improving and it will get better. There were a few nerves at times but we went into the match unchanged and it was not easy for them playing in such searing heat. “