'replenish drones automatically' doesn't seem to be a thing for supply ships that I can see in the Individual Instructions tab. I have had automatic resupply set to high on my normal save, but I don't believe this setting is a factor, and will continue to test as such. In my normal save, I do have the resources to build more drones on the supply ship, and the cash to buy more, but not subordinates.
I created a Before Save using a custom game start with what I believe should be all the necessary pieces for testing, so that the testing doesn't interfere with my online save.
https://www.dropbox.com/s/s32u51rah1lrr ... re.gz?dl=0
This save I ordered my Pelican buy 250 advanced sats from my honshu:
https://www.dropbox.com/s/fui67rphnwlt9 ... er.gz?dl=0
This save is during the transfer of the 250 sats:
https://www.dropbox.com/s/pzlxbr6i7bu0k ... er.gz?dl=0
^Loading this I was unable to replicate the bug, so I tried OOS:
https://www.dropbox.com/s/qkhqvnwn4xxnf ... OS.gz?dl=0
^This also didn't manage to replicate the bug, but I had other ships lined up to test in this custom start, so I ordered the Gorgon to buy various drones from the Honshu, and sell them to the basic claim station:
https://www.dropbox.com/s/snwoxybb66pt4 ... on.gz?dl=0
^"Last order could not be completed" with the gorgon, when loading the above save. this is part of the problem. I then ordered the Phoenix to sell all of it's mines to the honshu, got back in the discoverer, and flew it OOS. I saved again, while the phoenix was docking:
https://www.dropbox.com/s/kujp4ioz47y6x ... es.gz?dl=0
^Again, I wasn't able to replicate the problem loading the above save, so I saved again after the start of the transfer
https://www.dropbox.com/s/8w2dgsyxt4unz ... er.gz?dl=0
^Again, I wasn't able to replicate the problem, so I additionally ordered the phoenix to buy all the laser towers, mk1 and 2, and defense drones it could carry that the honshu had.
https://www.dropbox.com/s/npicga2otydzs ... er.gz?dl=0
^Loading this save, so far so good, the transfers are still going, but to throw a wrench into things, I ordered the pelican to buy 9 cargo drones from the honshu and 1 repair drone while it was busy with the pheonix. This order immediately failed, because cargo drones were somehow not available, even though he honshu has 30. this is another piece of this bug:
https://www.dropbox.com/s/m805arlhqv1yf ... es.gz?dl=0
^loading this save ended the mine transfer and a "Last order could not be completed" message was given for the laser towers, which were not destroyed, but not transferred either. Again, more buggy behavior with this command, so I canceled the undock orders from both the pheonix and honshu, and ordered the phoenix to buy the laser towers again:
https://www.dropbox.com/s/zmrvnboh56f74 ... in.gz?dl=0
^loading this save "last order could not be completed" for the laser towers again, none were transferred, and none destroyed this time either. I don't fully understand the circumstances that surround the destruction or duplication of consumables with this bug, but "last order could not be completed" when loading a save I know is a major part of it. I am out of save slots now, and patience for testing this, but hopefully that should be enough for you to investigate. Perhaps it was the pelican trying to buy drones that caused it to fail for the phoenix? If resupply was on, situations like this could arise naturally.
Note that all of these are transfer wares commands, not resupply commands. so consumables should have been coming from the supply ship's own, well supply, and not being made by the supply ship (this save doesn't even have consumable blueprints)
Additionally sorry for being a Bad OP and taking long times between updates, I have been doing some travelling lately. and it's hard to test things with this game without being at my pc to play it.