overdraft protection

Not sure I am understanding about the 3 separate transactions thing, but it sounds to me like they were treating each one separately, hence the 3 separate overdraft fees...

What you are probably talking about is that two of the transactions, being smaller, should have been covered by your balance, but that is not how most banks operate. They treat your larger transactions as priority, deeming them more important because it could be something like your house payment, and as priority, they attempt to clear them first.

So they cleared the large transaction first, which over drew your account leading to the other two overdraft fees.

I imagine if you had approached the bank manager civilly, which it does not sound like you did from the tone of your post, he would have reversed two of those fees, however, he is not obligated to do so. It is your obligation to learn the rules and policies of your bank and banking account and to balance your checkbook.