Bought a 16GB Moto X Style, 3GB seems to have disappeared.

Screenshot

Total used is around 2.5GB, but my phone says 2.5 GB is used. (See the screenshot above)
My media and everything else is migrated to my SD card formatted to internal mode.

I had this problem of missing storage space even before I formatted my external SD as internal.

I am running fully stock Android 6.0.

Please help.

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