I'm pretty sure it has something to do with the chain of custody of evidence. The methods and results of the search are 100% the FBI's responsibility, and they simply can't trust Verizon to do it right. It's the sort of thing that an appeals court would tear apart in an instance.
Can this be fixed in statute? If not, why not? The method and results should well defined and reproducible, right? It could even be possible for the FBI to have some level of oversight without actually having access to the data.
The fact that the numbers were all present at the robberies doesn't imply that the owners of those numbers are guilty. It's merely a lead. The result is just records anyway, the very same that the FBI would get from a more permissive request.
The only thing at risk is that the carrier would mess up the query. But if anything FBI could provide the SQL/whatever query as well.