More myki mischarging on Vline

So this weekend I travelled down to Geelong from Hawthorn, and then back via Lara.  I was travelling on my zone 1 33 day myki pass.  I was also travelling with someone who was using myki money.

Because I was travelling on myki pass, I should pay less than the person travelling on myki money.  My pass should contribute something to the cost of the Vline Fare.

To cut a long story short, I was charged a total of $11.70 on top of my zone 1 myki pass.  Here's all my travel for that day (click on the image to zoom):

To cut a long story short:
My travel in Melbourne was free, because I was travelling on my pass.
Travel from Melbourne to Geelong was $4.20, which seems correct, my pass contributes $3.50 to what would normally be a $7.70 fare.
Travel from Geelong to Lara was also correct:  $2.10.
Lara to Melbourne?  Should be free.  Lara is in Zone 2, and my myki pass should cover travel in both zones 2 and 1 at the weekend because of the $3.50 weekend daily cap.  But, as you can see above when I touched off at Southern Cross at 17:33 I was charged $5.40.  Which seems to make no sense whatsoever.

But, it gets worse.

My partner was travelling on myki money.  And my partner was only charged a total of $7.38 for the entire trip, with no myki pass to contribute towards the cost of his fare!  Travel history below:

So he was actually charged less than a 2 hr zone 1-4 2 hour fare for the entire return trip travelling on myki money, which is meant to be the more expensive option. 

I'm certain if I query this with myki that I'll get a refund.  But the obvious questions are:

1) why is this happening at all?  myki has been running for almost four years now.  The excuses that "it's new" and "the bugs will be ironed out" simply don't wash any more.  They had three and a half years to get Vline charging right, but it doesn't appear that's the case.  

2) If I don't query this, am I likely to get an "auto refund" as has happened with overcharging in Melbourne before?  I doubt it... I simply don't trust that the system is smart enough to look at my travel history at some future point and work out that I was overcharged.  

3) How many other people is this happening to, now that, ostensibly, the myki rollout is largely over?

Of course it appears my partner was severely undercharged, with a daily off peak zone 1-4 fare being $15.40, so in reality we're kind of ahead anyway!