The Addicks were far from at their best as a pair of Yates penalties and a strike from Matty Virtue continued their dreadful recent record at home.
But it was Yates’ fall to the ground under apparent minimal pressure from Ben Watson for the third goal that angered Bowyer the most.
He said: “Have you seen the second penalty they’ve got? It’s unreal. The worst decision I’ve seen in my life. The fella just dived on the floor.
“That was horrendous. We’ll get an apology, but it doesn’t help me and the team. We have to improve, plain and simple.”
Charlton also had two men sent off in the second half – skipper Darren Pratley and striker Chuks Aneke. Bowyer is expecting the latter to be overturned.
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