i was NSF last year, and i was also amazed at this bug. but at
least it doesn't deduct anything more. 
i wished i had more time to investigate this but i ord alrd.
i reckon it may have something to do with the time u boarded it,
but it still seems that there is no fixed pattern. sometimes adult
fare, sometimes minimum fare.
and it seems that it is only possible to happen on an all-SBST
journey (no time to confirm, not so rich to take bus everyday to
test) where you are eligible for the $1.90 fare cap. i suppose
that's where the bug came from - there's an error in the coding of
the $1.90 fare cap.
another thing, if u were charged minimum fare for your first trip
in a 4-trip journey, all ur transfers are $0.39 (minimum fare minus
transfer rebate). that is confirmed.
if on ur first trip they charged adult fare, it'll be adult fare
all the way, though there's the $1.90 fare cap if it were all SBST
rides.