I have no way of knowing if this is a bug in Tom's Storage or Relics but most items from Relics cannot be extracted from inventories with Tom's Storage. (1.2.16)

Edit: I did some testing and found that Lore Fragments from Enigmatic Legacy also cannot be extracted by Tom's Storage.

I can add that servos from Industrial Revolution cannot be extracted, but at this point only this one item.
Server logs don't show any error.