Passport is issued by Deparment of State (DOS).
Certificate of citizenship is issued by United States Citizenship and Immigration Services (USCIS).
The burden of proof is typically on petitioner, even if data is in USCIS system, which it may not be, because the kid never applied for N-600.
Some people got passports erroneously (you can google news) and were denied passport renewal decades later after having passport for most of their adult life.
USCIS may (not saying they will) need to establish fact the spouse was US citizen for 3+ years. I know, passport is 5+ years, but it doesn't say exact date somebody became a citizen unlike certificate of citizenship.
Not saying this will be a problem for sure, but there's small possibility.