The article doesn't mention specifically what part of the Patriot Act is being questioned here. As I see it someone made bomb threats over a phone. Those phone calls were traced back to a specific IP, they probably subpoenaed the records from the phone provider which provided the IP for those phone calls. Then it's simply a matter of determining who was utilizing the IP during that time frame which can be obtained from the ISP. These are all actions I would expect to happen even before the Patriot Act, Yes?
Lundeby told the officers that someone had hacked into her son's IP address and was using it to make crank calls connected through the Internet, making it look like the calls had originated from her home when they did not.
The only way that is possible that I'm aware of is they went through a wireless router, happens quite frequently as many people never secure them. Anyone can connect if they are within range of it.