Ernie may right in some calls but the handball by Jakobsen was not for the Assistant Referee to call from his spot as it was not his zone.
 From the TV replay the penalty should have been awarded and really depended on Kurt Ams being in a position to see it.  I would have look at the replay to see if he was in a good position to see it.
The handball rule is based off last season's rule since the competition started before the recent change so he may have called it as ball to hand.
This is where you need an Additional Assistant Referee not positioned by IFAB dictates but on the opposite side to assistant ref running the line I.e an assistant ref on both sides of the goal.

Merrick hasn't got rid of his soured faced persona in 15 years.  Piss off.

Firstly that rule change was in effect from March 2019 ..when did the FFA Cup start ? I would think well after then.
Secondly I have not seen the handball situation but under the new rules if he made his body unnaturally bigger (ie had his arms out unnaturally ) then it should be a penalty .If his arms were below his shoulder and his arms were not in an unnatural position ....and in the eyes of the ref it was not deliberate handball .....no penalty .
The rule has not changed much at all ....the changes mainly affect goals scored through handball or goalscoring opportunities through a handball ... defenders handballs laws are are pretty much the same as they have always been .The main change for defenders is if their arm is above shoulder height it is now automatically handball .
There is a good explanation of it here... https://soccer.nbcsports.com/2019/06/02/new-handball-goal-kick-and-free-kick-rule-changes-now-into-effect/

BTW "Ball to hand" still applies under the new changes . "If the ball comes off the player’s body, or off another player (of either team) who is close by, onto the hands/arms it is often impossible to avoid contact with the ball"   This is from IFAB

The rules may change in March but they do not come in to effect until predetermined date in each country. There’s a variety of reasons for this including competition integrity but also allowing enough time for referees, coaches and players to interpret and train with the new rules 

In Australia the NPL, FFA Cup and all other forms of football continued with the rules as they were at the commencement of the 2018/19 season. 

The HAL will commence the 2019/20 season with all the new rules which will then be followed by all other competitions. 

This was confirmed on Twitter by Ben Wilson, outgoing head of referees at the FFA 

Aha feel like Merrick should have watched some footage before just believing what Hoolahan probably told him happened as that was clearly a fould on Kitto. Clumsy and unintentional but still a foul.

Kitto was the one who had possession and I don't deny the contact hurt Hoolahan it was still a foul to us.

Crap like this just negates any of the true things he might have said and just makes it come across as sour grapes.

Also Mileusnic would have had a clear pass into the net despite there being two Jets players running back. I was in a perfect position to see that one unfold and just saw the replay.

Whether its an obvious goal scoring opportunity when its Mileusnic is another matter aha

Again, it was just stupidly clumsy by Italiano but he did clip him and running wide is a bit of an exaggeration as he was on a clear path towards a left foot pass into an open net. 

The handball I didn't see and can't find a replay but have heard it should have been a penalty so 1/3 Merrick isn't too bad.

This. No idea where Ernie gets "kicked from behind" from when Kitto was in front of Hoolahan. 
Obviously not good for the Jets having one of their new players out for 3 months, but you should be sure of what you are saying before you say it. 

The ref had no chance of seeing it. Jakobsen's back was to the ref and the incident happened so quickly as well.

Well said ,your spot on. Merrick 1/3. It was a definite penalty but from where the referee was standing he might have been unsighted.