Jon, we had a 16 year old kid have almost the same thing happen a couple of weeks ago. He went W2W and nose dived the other side. His body hit the water and made a thud that I have never heard before (I have participated in recreational watersports for over 20 years). I knew he was wrecked, and when we circled back, he climbed onto the platform and had blood in his face. He had a gash (not as serious as your wife's), and all I can think is his head hit the board during the fall or right after.
Your wife almost certainly did not have enough speed for water to gash her head, so my guess is the board hit her head or she hit something in the water. A fall like that can leave the rider disoriented and much can happen without realizing hit.