The 22-year-old Dutchman admitted a Football Association charge of violent conduct after kicking out at Sheffield United midfielder Michael Doyle during his side's 2-1 victory at Bramall Lane last Saturday.
Referee Andy Woolmer did not see the incident but Emnes was later charged on the basis of video evidence.
Mowbray told the club's official website: "The bottom line is Marvin does kick the boy but you and I know Marvin is the quietest lad you will ever meet in football.
"But look at the provocation he's had, not only in that incident when the boy gouged him in the mouth, but he'd been pulling his hair all game long and that's the problem with retrospective refereeing.
"I can't defend Marvin, he did kick the boy. But where do you stop retrospectively refereeing football matches?"
Source: PA
Source: PA