So, I don't have any consistent way of replicating this, but I do have a few theories as to why it happens.

If you have an auton bay (not restricted to constellation class), there's a bug that duplicates your either active, or inactive autons. So far it hasn't happened for both for me, but that might change in the future. It has duplicated only a fraction of the total autons, regardless of how many are active/inactive. It has also done it on the same auton multiple times (such as one instance of me getting 5 of the same auton, with all of the same equipment/name).

When this occurs, not everything duplicates. Things that do include:
Name (Sometimes)
Weapon (Sometimes)
Armor (Every time so far, might change)
Shield (Every time so far, might change)
Auton type (Every time so far, might change)

The most common times this bug occurs is when I go through a stargate. I have noticed it once without going through a stargate, but that might be because I just didn't notice it earlier until then, so it *might* be stargate only. I would like to specify that this bug is seemingly rare, as it's only happened to me 6-7 times so far, out of many attempts at replicating it and doing playthroughs. (It should be worth noting that at least two of the times, I had autons in my bay with damaged armor repairing when I went through the stargates when this occurred, though I have no idea if it is connected.)

Sorry for a lot of uncertainties and reading, but that's all I have right now. I will add/update this if I come across anything new and/or concrete. Thanks for reading, and I wish you the best of luck in finding it!

(Side note, this was all on Vanilla+CC, no mods on 1.9 Alpha)

ironparrot 8 May 2020:

Just had a Auton dupe, weapon duped but armor and shield were reverted to stock.

george moromisato 28 Aug 2020:

I can't reproduce this, but I've added debug code in 1.9 Beta 2 that will hopefully help us track it down.