Since she is in San Diego, I presume you are driving or walking back into the US? Mexico does not request documents for casual visits under 72 hours, and don't ask for anything when entering.
The question is "what is her citizenship?" If she has a US Passport, no problem.
If she is a Japanese citizen then you need to find out what kind of visa was required for her to enter the US. If a visa was required to enter the US, then what kind, and what are the terms of that visa? Please re-affirm the conditions of her visa.
If she required only a passport to come from Japan to the US in the first place, and all she used was a Japanese passport... then the same Japanese passport will suffice to enter the US from Mexico.
But please make sure that there are no visa restrictions.
Also... any proof of her residence, marriage, etc., may come in handy... but that's just for extra measure. Answer only what they ask, and don't lie about anything.
I live in Baja.