IPhone – No Data via Cellular iOS 10.2

You need to also turn off background updates, which is where the bulk of the data usage is likely occurring.

Settings> General > Background App Refresh > Background App Refresh Off. Of course, you can choose which apps you wish to turn off individually for background refresh instead.

Don't forget that if you are worried about cell data usage, you can also put your phone in Airplane mode, which turns off all radios, but then manually turn on Wifi. This will force your phone to use only Wifi, as the cell radios are off. Simply turn off Airplane mode when you wish to use the cell radio again.

It could be something like this secret (well, not so secret any more) program as detailed in the Wall Street Journal:

Updated Nov. 13, 2014 8:22 p.m. ET

WASHINGTON—The Justice Department is scooping up data from thousands of mobile phones through devices deployed on airplanes that mimic cellphone towers, a high-tech hunt for criminal suspects that is snagging a large number of innocent Americans, according to people familiar with the operations.

The U.S. Marshals Service program, which became fully functional around 2007, operates Cessna aircraft from at least five metropolitan-area airports, with a flying range covering most of the U.S. population, according to people familiar with the program.

I've noticed the same thing myself, and I hear light planes flying over my greater NYC area home in the early morning several times a week. Because I'm a bit paranoid, I turn off my phone at night.