"It's so frustrating," said Johnson. "I had the same view as the linesman and he was guessing, while the referee could see the incident clearly.
"Jamie must miss the Forest game, but we can still go there full of confidence because this was somewhere near our top form.
"I felt we were poor in the previous game at Brentford and I've been a misery all week. Perhaps I should be like it more often because the lads have really responded."
Crewe manager Dario Gradi was also disappointed with the referee after midfielder Gary Roberts was sent off.
In a challenge totally out of character with rest of the game, Roberts and City's Louis Carey launched themselves for a 50-50 ball. Carey got there a split second before his opponent and escaped without even a caution.
Roberts was deemed to have gone over the top and was shown a straight red card.
Gradi said: "Having seen the incident on video, I thought both players should have been sent off.
"Everyone keeps telling me it was a great game, but I didn't think so.
"There were a lot of chances, but not enough for us. We were second best and, although the players worked hard we didn't pass the ball as we can."