Sorry it took me so long to respond!
Yeah, the actual transporting of ammo/fuel is done with invisible inserters. This saves a ton of UPS compared to doing it script-side. Unfortunately, it also means when I make a mistake in my code you end up with situations like this one xD.
If you use the mod reset hotkey (CTRL + Shift + Alt + Backspace by default), it will trigger an orphaned inserter check which will fix your issue temporarily. This check is also performed once every five minutes of game time, so theoretically it should fix itself, though there may be some reason the auto check isn't triggering. Regardless, you can use the hotkey I mentioned for now, and I'll look into the problem with bot deconstruction for a fix.
Thanks for reporting this issue. Let me know if you have any more questions!