If I am correct then it is intentional. When it's happened to me its after I sent multiple TX requests very very quickly back 2 back. I bet you could do a lot more damage if you used a script to request them faster than I was by hand.
The above said, its likely a small # of people doing this in intentionally. Cryptsy does prevent future withdrawals once your balance of any coin is negative, that is likely slowing things down but they need to figure out how other exchanges prevent this glitch and get it fixed asap.