Philippines doesn't have dual last names. However, it's the law to follow naming convention (Philippines Republic Act 386)
Middle name = Mother's Maiden name or None (if illegitimate child)
Last name = Father's last Name or Mother's last name (if illegitimate child)
It may not be very strict in US side of things. Since in US, middle name is just part of the given name.
But, It's pretty strict on Philippines side in terms of names since it's the law. If her DS-160 is incorrectly filled out and doesn't match her passport, make sure to have it corrected. If there are corrections in any of her documents, inconsistencies in her names, make sure to have it all listed in her NBI clearance’s AKA field.