Notary

Person A appears before the notary, signs the document.

Person B comes in later and appears before the notary, signs the document.

Notary only attests and names person B in the acknowledgment certificate. She does not list person A.

This appears that the Notary Public did not properly certify each signature and name the subscribing witness in the document.

Is there a penalty for a notary who does not properly notarize a document?

I do not believe there would be a penalty, so long as the notary did not do anything dishonest I do not see that there is a problem with the document at all.