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.