From the article:
"hadn’t fully assembled the proprietary machines used for the herpes study when the experiments began" ... "company underreported the rate at which the machines broke down during the study" ... "employee also alleged that some crucial parts of the devices ... were modified to improve their accuracy"
FDA is generally skeptical of validation data not generated from "production equivalent" technology, but they get even more skeptical if you tell them something is X and it turns out to be Y down the road. That (rightly) sends them on a fishing expedition.