You sure that it stores that or does it just store the fact that the flashlight was on in some log somewhere on the device. I could see the usage statistics of pretty much anything being stored in /var/log/<app access log> and then cross referenced with the location information that the phone already stores. The likely just correlated the two... in fact the location information is likely on no mater what and they could have used that anyway.
"Gainesville Police Department detective Matt Goeckel said the flashlight on Bravo’s phone had also been used on nine occasions that night, for a total of 48 minutes"
How can they get this information? I would definitely like to see what my phone has stored about me.
Possibly a log of system events?
If you have an android and enabled some kind of feature by mistake (like me, I always say no for these but it has my location, even when I was abroad) you can see the log here: