When you mine a raw resource the game picks up two items, the rock you salvaged and the resource it contained.
It doesn't know to look for available space for both items.
For example: if chest 1 is full but contains X and does not contain Y. Mining a raw resource Y that is inside the block type X will result in the raw resource being lost.
The game tries to put both both in the 1st chest because it sees X is there and therefore it can fit in it.
How to reproduce:
# link a salvage computer to 2 chests
# fill the 1st chest with whatever you want (do not fill with ores)
# make sure the terrain block you're going to mine is in that chest
# mine that terrain block that contains an ore
# notice that you gained the terrain blocks, but the ores are gone and can't be found in the 2nd chest.