In your case mind, with all phones passing their diagnostics, with there being no record in the system they were sent both on your end and the provider, I would of happily credited you the cost of the overages and a one time courtesy credit of "x" amount for the hassle it has caused you just to keep you in good graces with the company. What they did was utter bull and can honestly of had them fired.
If you are being charged for "x" messages over the package and they can't prove or show them to you, you can't be charged for them if you notice it and call in. At the bottom of your bill for their Billing system and your online bill it will show you every message sent, what time, and to which number. The only thing they can't tell you by law and company policy is what number it was sent to. They are required to show you how to find that listing of messages to prove they were sent, which is perfectly allowable by law and is mandatory if asked.
And yes that is an honest reply, but that is how I would do it. There may be other CSRs out there that wouldn't, but as long as the call is at least neutral the majority of us are just so happy to not be yelled at we will do close to anything to leave you happy.