Gatland questioned some of the refereeing decisions, including a James Botham second-half score that was ruled out for obstruction.
Captain Dewi Lake said Wales “got their details right and the officials made the call”.
“I need to get some clarity on the disallowed try from the maul, we would have had a conversion to go in front,” said Gatland.
“It’s where we are at the moment – we’re not getting any 50/50 calls and we just have to work through that.”
Australia head coach Joe Schmidt is adamant the right decision was made by French referee Pierre Brousset and his officials.
“It is really clear,” said Schmidt.
“The law says whoever rips the ball has to be connected to the jumper and there is clear air there.
“There are four match officials who made that decision, not me, so I will just leave it with them.
“It looked pretty unequivocal in their mind. Those are the decisions we do not have any control over.
“Sometimes things happen and you just have to get on and play the game.
“I had some experiences last year where you felt you didn’t get the rub of the green and you just have to wear that and get on with the game.”
