Stanley were beaten 1-0 in front of a crowd of 13,387 at Fratton Park but the Reds players were furious by a challenge on Murphy by Portsmouth’s French midfielder Romain Padovani on the half hour mark.
Referee Chris Sarginson opted to show only a yellow card for the tackle and Beattie believes his side have found themselves on the wrong end of a number of decisions in recent times.
“I think the lads are not happy with the ref’s decision not to send Padovani off,” said the Stanley boss.
“I looked at the video and it’s a joke of a decision. He’s stood right there.
“I was lucky I wasn’t going to see Peter Murphy in A and E with a broken leg.
“The ref took too long to make the decision and he’s thinking I don’t want to be battered by 15,000 fans for the rest of the game, so he’s given him a booking.
“The lads were unhappy with the nature of the tackle, they were incensed and I think they had every right to be.
“Their discipline for me is second to none and coming in the face of some of the officiating we’re getting at the moment, it’s massive credit to them.”
Defeat saw Stanley drop to third bottom in the League Two table ahead of Saturday’s trip to Burton, although they remain five points clear of the relegation zone. But Beattie insisted his side deserved something from the match.
“I was very pleased with the performance,” he said.
“I thought we restricted Portsmouth to no shots in the first half and then one mistake and the lads have been punished.
“But the reaction to the goal further cements my feelings for the side and I think they were desperately unlucky not to get something out of the game.
“One of the only mistakes the lads made, they got punished in the most severe way.
“But I can’t fault their effort, they performed really well and the best side lost.
“We played some great stuff, we got the ball down and the lads have grown so much in confidence.
“It’s not every week they play in front of 15,000 but they played some great stuff.
“Sometimes you don’t get what you deserve in football.”