Shane Watson, Mitchell Johnson, Usman Khawaja and James Pattinson were all penalised by the head coach after failing to turn in a questionnaire asking how their performance could be improved on the sub-continent.
Watson has subsequently left the tour, stating that he is "weighing up" his international future.
Arthur's move has been met with derision from former players and pundits alike, but Clarke has said that there is more to the situation than meets the eye.
He claims that the four players have let the team down and shown a lack of respect for Arthur.
"I want the public and the media to understand it's not just about one incident," The Telegraph quotes the 31-year-old as saying. "On this tour our performances have been unacceptable and there has been some stuff off the field.
"We were asked to do one thing from the head coach. It was giving information, about not only improving your game – what you've learnt from the first two Test matches – but also how can you help this team turn things around.
"For the four players to not do it, not only does it let the team down, it also shows a lack of respect for the head coach."
Australia trail 2-0 in the four-match series.