It depends. If the company you have bought from have had a massive amount of fraud that they have processed or a lot of chargebacks, then I don't think it is over the top for the credit card firm to be cautious. But if it is a general purchase, then it is. But we may never know!
I've never experienced my bank calling me to verify a charge. $49 isn't enough for my bank to bother me with verification. A charge in the hundreds range could warrant a call. If I were you call your bank or credit card company and ask them about not doing this in the future. It's possible that they may have an option where you can establish your own verification limit. For instance, you can tell your customer rep that you would prefer to be contacted for any charge above the price range $xx.xx, therefore they can update their notification records.