In some circumstances, myki is definitely overcharging you.

After running a little travel experiment today, I can now confirm that anyone following a specific travel pattern is probably getting overcharged. If anyone else wants to try it, I almost guarantee you'll get the same results. Times below are approximate as I wasn't recording them but I'll have my travel history tomorrow.  I'm travelling on myki money on a full fare myki(I have no idea if travelling on a myki pass would be effected by this, but if someone with a pass wants to duplicate my trip I'd be interested to find out).

1. I rode my bike out to Darling Station (in the zone 1/2 overlap), touched on about 2:15pm, starting a 2 hour fare product which would expire at 5.00pm.
2. I touched off at East Malvern (zone 1/2 overlap), was charged $2.26, about 10 minutes later.
3. I rode to Alamein (zone 1), touched on, about 2:30pm maybe.
4. Touched off at Hawthorn (zone 1) about 2:50pm. Got charged $1.02 to bring me up to the $3.28 for a 2 hour zone 1 fare.
5. Touched on again at Hawthorn about 3.00pm
6. Touched off at Prahran (zone 1). Charged nothing as still in 2 hour fare window.
7. At about 5.05pm I touched on again at Prahran
8. At about 5.26pm I touched of at Hawthorn. Instead of being charged $0.02 to bring me up to the weekend cap, I was charged $1.04.  So I have been overcharged $1.02 on top of the $3.30 weekend cap.

Now I know on trains this is highly unlikely series of events and will only effect a small number of passengers, but on trams and buses which are currently operating in the seemingly inaccurate "headless mode" where GPS is not always accurate and drivers are not setting routes on the myki equipment, buses and trams think they are in the overlap a lot more than they should.  It will effect a a fair number of people. What's more, it would appear this problem has been happening for some time, possibly since the beginning, as I know this has occurred to me before and I reported it at the time, back in 2010 I believe.

I'm sure anyone would agree there is simply no excuse that this is still happening, particularly now that the myki rollout is ramping up and metcard equipment is being removed.  I know I can report this to myki, and I know I will get my money back.  The problem is that if they are aware of this problem, they aren't doing anything to fix it.  Who knows what other bugs like this there are.  People should not need to ring myki (which costs money in itself) to get a dollar or so back.  And some people probably won't notice and will just get overcharged.  Sure, it's only $1.02 but hey I'd prefer that in my pocket than theirs if at all possible.

I'll publish more about this as it progresses.

EDIT here's an image of my travel history from the myki website this morning to confirm what I've said.  Again, the final charge of $1.04 should only have been $0.02.  I have raised a fault with myki via the website to get my money back but what a really want is a commitment from them that the fault will be fixed and that nobody else will ever get overcharged in this manner.