The same way other registries do. It isn't exactly difficult to determine fraud when there is a paper trail!
No one selling fake hets is going to register them, and wind up with police knocking on their door when someone finds out about it.

Registration means that person's identity is confirmed, and that animal's identity is confirmed, and it's all kept in a central database. That is more than enough to prosecute for fraud if someone registers a normal as a het. What's more, that individual would be barred from registering animals in the future, and all of the animals that they have registered would likely be removed from the registry.