Winger Scott Sinclair was almost struck by a glass Buckfast bottle thrown from the Easter Road stands during Saturday's William Hill Scottish Cup win over Hibernian.
"If this bottle hits Sinclair it could have caused a severe injury. He was lucky not to be hit. Too many times this season a line has been crossed.
"For me, I've always thought that Scottish fans are the best in the world in terms of creating an incredible atmosphere and fantastic noise. Without a doubt, this is one of the best countries in the world to play in for atmosphere.
"But a few fans are destroying the whole picture you get from the stands because of these coins and even a bottle being thrown at the players."
Ajer added: "That is completely unacceptable and a real shame as the majority of the fans here are among the best in the world. To see these situations being the headlines is really quite sad.
"These incidents need to be taken of. They are not great for Scottish football and I hope some action is taken.
"I think it's important to explain that the majority of Scottish fans and people are fantastic. Hopefully the few bad incidents can be taken away."