Have you checked your "Recently deleted" album? Maybe it takes up your storage. You can read this thread:
https://forums.macrumors.com/thread...ne-storage-almost-full.1951573/#post-22495360
You are running iOS 9.2.1, it's the latest version. So it has no association with system. Maybe you can try to use professional tools to clean up space for your iPhone.
iMyfone Umate is a program which can free up space with more than 25 analyzation techniques and technologies(I read this from lifehack). If you don't want to do like this, you can try to back up your data first, then deleting all data and reset your iPhone, at last, restore your iPhone. Hope this helps!