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:

1. link a salvage computer to 2 chests
2. fill the 1st chest with whatever you want (do not fill with ores)
3. make sure the terrain block you're going to mine is in that chest
4. mine that terrain block that contains an ore
5. notice that you gained the terrain blocks, but the ores are gone and can't be found in the 2nd chest.