not a big deal! don't worry

Make an appointment with local immigration office. They will correct your daughter's I-94 easily.
I have an officemate, whose wife was H4. Did not notice her I-94 was given only 3 months of entry (should be same as the length of H1). Till she realized the problem when she applied for F1. It had been more than 1 year's out of status.
She made an appointment with local immigration office and got it corrected rightaway.
It's CBP's fault, not your daughter's fault.

Don't worry!