Two issues if a concrete tile is accidentally placed inside of the factory.
[1] If placed on the lower border (eg. orange for the smallest building) the player can create a new exit for the factory and it obscures the belt/pipe access ports.
[2] If placed over the chests and then picked up again, the chest disappear and cannot be recovered or accessed.. the build losses them permanently.
Tested in: Ver 2.1.8 (and prev.)

The ability to place concrete out of bounds is an unfortunate interaction with the water-fix mod (you have Alien Biomes installed, I assume?). Nothing I can do about that, just try and avoid placing concrete out of bounds if you can.

I can however do something about the missing overlay chests thing.