DOFF assignment has 2% chance to crit fail. Item has 88% chance to improve quality on upgrade. DOFF assignment crit fails and item doesn't improve.
That is all.
Actually, that's -not- all. This kind of trend is just steps away from a big "F U!" from the game. "All that effort you put into building a decent DOFF deck, all those resources you spent on crafting the Super Double Plus Superior Experimental Upgrade Token, all for naught. I say you lose because I don't want you to progress." Now, obviously, the game itself can't tell me this. That would be silly. But so is the random number generator. Infinity doesn't stop at 12!
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So, i tend to not even worry about it, it is likely their way of getting us to spend more and more and more dilithium on it and when it comes to crafting after crafting over 500 warp cores just to get a W>A or something that helps my ship out and never getting it, i just gave up with it....i am not wasting resources because the developers can't be asked to get off their butts to actually make an effort on a game that they want people to put money into, eve though its purely free to play.
I don't even bother with Duty Officer TRIBBLE, i find it a waste of time that hardly ever pays off.
(RE = reverse engineering - destroy an item with a chance to get a schematic for a better one).
P.S. Last time I calculated, to guarantee a gold item in STO with the current upgrade system you would need ~800 million in upgrade mats.