Too many unreachable item/material/resources [UPDATED with root cause]

Update : Found the root cause of this bug. 

Apparently I have tear out the first few roof of my storage area connected to the main building with 2 floor (2nd pic) OR tear out the wall connected to the main building (3rd pic).

Unreachable coin when storage with roof & wall connected to main building

Reachable coin (and wood outside) after disassemble first few row of roof

Reachable coin (and wood outside) after disassemble 2 wall connecting to main building

Too many unreachable item even though they are at the same layer (-2) and villager able to walk there (not controlling the character)

Crafted item unable to reach in my own house, have tried building new floor, removing it, and digging down.

Log unreachable even though the copper beside able to reach

Tamed slaughtered cow unable to reach, both inside and outside pasture. Removed wall, fence, door still unable to reach

Coin on the floor unreachable