The warrant in question is one that allows them to deploy the NIT in order to get the IP addresses in the first place. They wouldn't know these addresses prior to deploying the NIT, so there's no way they'd be able to get a warrant for each IP prior to that. Once they had the IPs, they subpoenaed the ISPs and got search warrants for the owners.

I haven't really made up my mind about the legalities of this case, it's quite tricky. I think the FBI should definitely have to disclose the NIT (both the exploit and the payload) to the defense, but I'm not sure about the warrant (Rule 41 issues aside).