Ray,
I'm not really sure where your professor is going with that remark. If a provider is not paid what they are suppose to be paid and it is written in the contract, then they need to contact their provider rep and ask why. I'm not aware of any billing software that would recognize if a payment wasn't correct specific to a particular contract. The only way to know that a claim wasn't paid according to the contract is for the person who is reading the eob to recognize it. They have to know the contract, and understand how to read the eob.
As a side note, I personally have not seen this happen very often. Usually the contracts are loaded into the carriers computer system and claims are automatically processed.
Good luck with your report.
Michele