I love this thread! I have either made the same mistakes outright or can see myself easily doing so. It is fun to laugh at these!
Anyway, here is another one which is not as bad as my other one. It had been many turns before I finally got the Last colonization tech and I really needed to colonize those gas giants in my 12ish systems. I quickly "copied" my rock colonizer, changed the design type to Gas Colonizer, but forgot to change the colonization component from rock to gas. Then I splurged added my new gas colonizer to all available construction queues. Didn't notice the problem either when the ships got built - they had the right name, right? All on the same turn I got a bunch of "Cannot Colonize" errors, but by this turn the 2nd batch of wrong colonizers was produced, so I had to retrofit (at great cost in resources and time) 20 to 30 Gas Colonizers to remove the rock colonizer component and add the Gas colonizer component. This bothered me so much, I didn't even check my resources that turn and (you guessed it) the mass retrofit took me into the red. I don't think any ships got auto-scrapped, but I did lose production at several planets that turn. Grrr!
Slick.