You don't know why the officer made the stop, and he is under no obligation to share that with your wife. That being said, the officer also could have run her plates and found that her registration was no longer valid, for whatever reason. Just because your insurance was then current does not mean the DMV recognized that and automatically renewed the registration, so it is still very possible that your wife should not have been driving the vehicle at that time.
Based on your post, I do not see any reason for the ticket to be dismissed, but your wife may, however, see some leniency from the court if she shows up with proof that she is completely in compliance with the law.
The only thing worse than getting into an argument about politics is getting into an argument because you refuse to argue politics.