The lack of technical information makes it impossible to answer. You need to ask the testers what concerns them. How do you know the car tests lower now than it did three years ago? If it failed emissions, this means it doesn't. The same parameters are measured as specified when the vehicle was manufactured. Your friend would have been given a printout with all the information.
As far as I am aware, the only thing that has changed with the new testing procedures is the requirements that a dynamometer setup be incorporated, and that a 'test only' facility be used on vehicles above a certain age (if so ordained by the DMV). Since results are transmitted directly to the DMV, cheating is much harder too.
Finally, if the issue is an incompatibility between the CIS engine management and testing procedures, mediation needs to be done with an appeal to CARB, and there would be a lot of interest in this case.