Murphy picked out Stoke, Blackburn and Wolves as the chief offenders for making "ridiculous" and "brainless" challenges and insisted that approach came from the teams' managers.
The Fulham midfielder said: "You get managers who are sending their teams out to stop other teams playing, which is happening more and more - the Stokes, Blackburns, Wolves.
"They can say it's effective and they have got to win games but the fact is the managers are sending out their players so pumped up there is inevitably going to be problems.
"Every ship has a captain and that's the manager who is in charge."
However, Potters chairman Coates insists his side approach the game in the "right spirit" and highlighted his side's position in mid-table in the Premier League's disciplinary lists.
Coates told Stoke's official website: "I am surprised by his comments. He himself is a very competitive player and maybe with hindsight he perhaps wishes he had said nothing, but there you are.
"We are a strong team, we are competitive, but we like to think we are fair and play the game in the right spirit. That's how it should be.
"If you look at the disciplinary league table this year, we are doing okay. We are sitting in 10th place and you will see in that league table some notable names below us and some red cards being shown to those notable names as well."