MagicalTux knows about this. There was a time frame shortly after re-activation in which absurd fees, sometimes millions of dollars, were calculated. It is beyond me how such a simple calculation can be done with such massive mistakes, but you can assume that they'll fix it within the next 24h. Otherwise, highlight MagicalTux in #mtgox on freenode during daytime in Japan.
Those "mistakes" are really absurd. I think it is safe to say that reasonable code cannot produce such errors with a single mistake; the consistency checks should stop things immediately. At least it never happened to me; I make mistakes, but the majority is caught by checks, and the rest by tests. Now I don't think what I do is special at all -- I just admit I do mistakes and take precautions to notice them in time.
A consistency check of the type "WTF I have a negative balance" is very easy! As is one that notices drastic changes in absolute value of all accounts, though that one might be executed asynchronously and thus take a few seconds. (Seconds! Not "lol an error happened half an hour ago and I just noticed via complaint on IRC")
It's really wild-west hacker programming. I cope with it because I got zero-fee for a month and know how to annoy the admin if errors persist. If this doesn't improve soon, I will call it "too risky" and leave the exchange though. We've had another error tonight, orders not being executed. That might be even more dangerous than the fees, because it produces errors that cannot be fixed in retrospect (can't execute order afterwards!).