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."
Not surprisingly, United boss Jackie McNamara, who is doing his best to keep his young stars focused on maintaining their phenomenal form and under contract at Tannadice, was delighted as his team claimed their fifth consecutive win, in each of which they have scored at least four goals.
He said: "The players haven't spoken about scoring four goals in games recently, they are just interested in keeping going to the final whistle.
"We are always confident of scoring, whether in the first minute or the last and even when the subs come on the are keen to get involved and grab a goal."
Although it took three goals in the final 15 minutes to finally overcome Kilmarnock, who played three quarters of the game with 10 men, McNamara had no sympathy for the number of yellow cards the opposition picked up.
He said: "The elements made it difficult and we told the players at half-time to keep playing football and moving the ball quicker as the play was condensed in the first half.
"Obviously that led to a lot of bookings but I don't think Kilmarnock can have any complaints as we have turned their players and the referee was been spot on, including the red card as Stuart Armstrong was twice getting away from his opponent."