The central defender has received a four-match suspension and £40,000 fine for his actions after an FA Cup defeat to Norwich in March where Dier's brother became involved.
An independent panel ruled that Dier's behaviour was "objectively threatening" and it was not his sole intention to protect his brother.
The spectator involved told police in a statement that he was acting like "an idiot" and did not feel threatened and reiterated those feelings to Dier at their meeting, which Mourinho thought would have been enough for a "fair decision".
"They don't have the know-how, and it's very, very difficult to lead something when you don't have a clue about the world that you are leading."
Mourinho has been defensive of Dier from the off and said he would not agree if the club also decided to punish their player.
It has been revealed that any internal action was postponed until the end of the Football Association's disciplinary process, but the Portuguese's position has not changed.
"An internal action is an internal action that I don't think we need to share," he said. "I have no comments about it.
"You know, even without me answering direct to the questions, I think you know my position in relation to what happened. I would prefer to say in relation to what didn't happen."