In general, if a ship retreats, there shouldn't be much of a problem. Just because some players don't like it, doesn't mean it's unacceptable. I'm especially accommodating when the player has almost no chance of getting additional experience. If the last BB is fighter camped and heavily outnumbered, the only reason not to retreat is extremely good sportsmanship. And if the BB does, it's his opponents' fault for not giving him a chance to fight back. If the last CV has no planes or is a camped BW, it's perfectly fine to see no reason to feed the enemy's experience gain for not only no personal benefit, but a loss.
The only places I see issues are Occupation and GB2. In GB2, I've seen CVs screw over their own teams by retreating. And there's an occasional instance of exploiting Occupation's issue to spite the other team. For those kinds of things, I'd happily punish players. But for the rest: not so much.