Dundee United made heavy weather of making it five consecutive wins, claiming an incredible 21 goals in the process.
Gabriel Reuben was sent off after 22 minutes with a rather harsh first yellow card followed by a second inside five minutes, reducing the home side to 10 men with three quarters of the game remaining.
Johnston was frustrated with both the performance and Reuben's red card.
He said: "It was always going to be a hard game against a confident United but I didn't think there was much in the game before the sending off.
"The first booking was harsh and I think perhaps the referee was too keen to get his cards out.
"I can't complain about Gabriel's second booking but going down to 10 men is frustrating and spoils the game for everyone."
Johnston asked referee Euan Norris his opinion about the ordering off and his decision to deny his side a penalty but with no joy as he explained: "I asked him about the double booking and also at 1-0 when the ball hit a United player's hand.
"But he said it was unintentional, but both of them were big decisions."
However, the Killie boss was proud of the way his 10 men held on for the best part of an hour before collapsing - although he was keen to point out the scoreline flattered the opposition.
He said: "It was a great effort from the players who worked extremely hard.
"But we have switched off for their first goal and after that we were a bit naive.
"I was disappointed in the end but I don't think there was a four-goal margin in it."