DracoSys

I'm positive it's mod-related. In my experience, vanilla salvaging order will constantly salvage until 0 (valuable) targets remain. I don't know much about modding this game or Lua but I can tell that the mod manages its own targeting index (depending on the command). Based on this previous comment, I'm pretty sure this is the reason Carrier Command manages its own targeting rather than using vanilla salvage targeting:

In my experience in singleplayer, multiplayer, and dedicated server, this happens every so often with salvaging regardless of leaving sector. I'm confident it has something to do with targets/target indexing in the mod as it seems to happen more often during fights and when 1 set of fighters salvaging fully destroys a target. Also, multiple ships being given Carrier Command: Salvage in the same sector causes this issue almost every time on one or all craft involved.