If the fare had the AP restriction, then it means you should have ticketed, not booked, before the deadline. In this case, I have a feeling that you share 50% responsibility for not keeping the deadline. Nevertheless, the agent should have double checked the amount charged. At least, it's good that they bent the rule and got you the low fare. It looks like UA overrides AP rule occasionally for one day.

I had a similar incident few years ago. Purchased nine-segment trip and the agent quoted it was USD200 using one fare basis. Upon ticketing, she confirmed again that it was USD200. The next day when I checked my account, more than USD300 was charged. So I contacted 1P desk, and was told that Apollo automatically applied three different fare basis since Apollo is not capable of auto-pricing more than eight segments. They refunded difference. Had I had not enough balance in my account, my account would have gone overdraft too.

As for overdraft, it's always wise to keep enough money in account. Last month, my account went just about negative USD5. But as a result, I was charged USD75 for overdraft fee. Also, they charged USD5 every business day as extended overdraft fee until I deposited fund although I couldn't make deposit earlier since I was out of the country. I lost like USD100 in total, so your case isn't too bad.

If I were you, I would call contact bank on the phone or visit its branch. In most cases, they are willing to reverse the fee, if it's not too much, into your account. USD35 isn't too much.