I pretty much always get random "other charges" taken from my card afterwards (on pre-paid bookings). I always complain, they always apologise for the "mistake", they always refund me.
And this isn't all the same airport or even country! There's clearly more to it than the same "mistake" happening over and over...
Another story: I used my "free weekend" voucher recently and I ended up paying something like £150 instead of something like £190. Apparently it only makes the most basic fare element "free" but you still have to pay lots of random location charges, extra charges, other charges,...