In their grand final replay at AAMI Park on Friday night, Melbourne suffered a similar fate to last year's title decider, giving up a big halftime lead to lose to Brisbane 18-14.
Munster wasn't blaming the defeat on the refereeing, saying his team blew their chances against the reigning champions.
But the Test five-eighth was critical of the standard of refereeing during the opening three rounds, most pointedly over the six-again rule which was changed in the off-season.
Looking to keep the ball in play for longer during games, ruck infringements and offsides from the 20-metre line instead of the 40-metre line now result in set restarts rather than penalties.
Heading into round three, referees had awarded 78 per cent more six-agains (9.8 per game) than at the same time last year (5.5 per game).
There were 12 set restarts in the Melbourne-Brisbane match, with the teams awarded six apiece.
"I love watching rugby league, I watch every team play and sometimes I just scratch my head watching some of the decisions in the bunker," Munster told AAP.
"I'm sitting here frustrated, I'm sure there's a lot of other people in the game frustrated, but they probably won't come out and say it.
"I'm going to put my balls on the line and say, 'We just want more clarity' - that's all I need.
"If we can get more clarity, then I'm sure a lot of people won't be whingeing and moaning about the decisions that were made."
Munster said he wasn't alone, with other NRL players sharing his view about the rule change.
"You just don't know sometimes as a player what the six-again are about ... I've spoken to a lot of players in the last three weeks and they shake their heads too.
"We sit down after games and talk about some of the decisions that are made for both teams and some of the moments we had tonight probably shouldn't have got and vice-versa.
"You see the six-again compared to last year in the first three rounds, it's chalk and cheese."
Munster was disappointed his team again let a lead slip against Brisbane, who banked their first win of the season after lacklustre showings in their opening two rounds.
The Storm had plenty of opportunity to regain the front-running but on the back of some poor decision-making and steely Broncos' defence, they were unable to get the job done.
In one late chance Munster was on the charge and attempted to find his flying winger Will Warbrick but his kick was too big and bounced over the sideline.
"They played big matches last year and that's the reason why they're in premiers last year and they scrambled well again tonight," said Munster.
"We had our opportunities and just weren't good enough - I wish I iced a couple of moments and I could have been a hero, but I ended up being a villain."
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