A good rule of thumb we try to teach referees is to do what competition rules/LOTG/procedure, etc. tell you to do and not create hypotheticals of what these do not prevent you from doing. In other words, keep it simple and straight forward.
But coming back to your specific question, if the referees' actions causes the game to deteriorate or brings other problems because of the argument created between him and the coach because of this issue, then yes, that will be an issue in the assessment. If not, then no issue. The question would then be, didn't you have other options other than to argue with the coach? Couldn't you include the fact that the coach was not following substitution procedures, provide the league with the evidence and move on?