I'm guessing there is a problem with a mismatch between her name in the Secure Flight data on each ticket and what is printed on her Nexus card. Could it be that her middle name is on one but not the other? There was a recent memo about this from the TSA to the airlines.. a lot of people with Known Traveler ID's have been rejected for PreCheck for this reason (apparently)... myself included.

It doesn't necessarily matter that the boarding pass itself to have an exact match of the name..just be sure the Secure Flight info for each of her itineraries has the name matching exactly with what's on her Nexus card and be sure the Known Traveler/PASSID is on there as well.