I thought what they were doing is applying all your debits, charging you if that puts you into overdraft, and then applying any credits. If they applied the credits first, you wouldn't go below zero.
Either way, you're trying to charge $46 against an account with $20, but one method results in 1 fee and one method results in 3 fees. The issue of credits vs debits you mentioned can compound this issue.
Consider a bank account with $20 in it, the day before payday, when you forget your World of Warcraft subscription hits today instead of tomorrow. That's $15. But you buy:
* Lunch: $5
* Coffee: $2
* Dinner: $5
* A late-night snack: $5
If the transactions happened in-order, the subscription causes the overdraft, and you're charged $25 or whatever (yeah they are very high). But in the way banks used to do it, they'd take your total ledger for the day, and order it by highest $ first. So, subscription first, $5 left. Lunch, $0 left. Coffee, dinner, and snack are three transactions when overdrawn, so that's $25 * 3 = $75 in fees instead.
Banks claimed that this process was because you'd probably want your highest-amounts paid first, as it'd be something like rent money. In the end, it means way more fees for them, though.
$75 in fees is especially brutal when you don't have much money in the first place; it pretty much caused me to not be able to even go to 7-11 for a candy bar for two months.