The FA slapped a three-match touchline suspension on the Addicks boss, who did not contest a charge of abusive language to referee Chris Kavanagh in last month’s win at AFC Wimbledon.
Bowyer started the ban on Saturday and will complete it after Burton Albion come to SE7 on March 12.
Asked about his punishment, he said: “It’s wrong, 100 per cent.
“On Saturday I guarantee you that when they [Doncaster] had a goal disallowed for offside, people said things they shouldn’t have done.
“So a three-game ban, I just don’t get it. I don’t know where that’s come from. I’m trying to speak to someone [at the FA] to get an explanation, because there is no reason to get a three-game ban in my eyes.
“I’ve seen other managers get sent off this season and get nothing [in terms of further punishment].”