For example, what if you have set up a bunch of auto-scaling instances to handle heavy load. During the middle of the night, your application suddenly goes viral in Indonesia or Brazil or some other large country in a different timezone from yours.
Your bill goes over its threshold - what does Amazon do? Do they terminate some of your instances (potentially losing production data!)?
The problem is that the exact times that "intelligent" bill-limiting features are likely to be used are the exact instances in which they could have absolutely disastrous impact if they make a mistake[0]
I haven't experienced this myself, but I've heard Amazon is actually rather lenient when it comes to waiving fees for clear mistakes (accidentally provisioning an expensive instance that you didn't mean to) - their customer support is supposed to be very good, though I have not had to use this myself.
[0] By "mistake", I mean that they are following your instructions correctly, but your instructions happen to be incorrect for handling this situation.