Maybe, although perhaps having BOTH sides contract over the length of a battle might be better, since sometimes you only seem to get out of place by being baited. Baiting/kiting is a legitimate strategy, just seems kinda harder for a player to bait AI vs AI baiting a person. Put another way, penalizing the early battle winner by making it easier to for the loser to retreat ships while still allowing for reinforcing might have unintended ramifications.
Or, in the case of SS, perhaps it maybe has to do with basically the following:
Ships in NPC fleets do have CR and it can be lowered through your actions, the terrain or in battle, it's just that NPCs don't buy their ships, don't pay for their maintenance (you could say they have infinite supplies) and don't care if they survive or not (unlike the player, who could be hurt financially or emotionally over a loss of certain ships). You can't wage logistic warfare against NPCs.
So perhaps instead game AI needs a more nuanced general retreat mechanic, wherein it makes more of an attempt to conserve at least hull %, FOR BOTH player and AI. Or maybe just always make the direct and tactical retreat order free, since on more than a few occasions I've had stuff die while waiting for a command point to retreat something, but the darn thing won't override an order to retreat on its own just to save itself. Not like we can also try the crew for mutiny...
Adding some code for CR conservation might also help, but seems just as likely to backfire; why bother saving CR for tomorrow when you might "die" today?
Further discussion in spoiler, but since only semi-related, seems better to stick into something that drops down...
Spoiler
A bigger issue is perhaps that game/battle AI has kinda the same issue that arose when initially testing neural nets with poker and betting. Since a lot of algorithmically procedural game-playing opponents lack a mistake heuristic (ie, they don't accidentally make exploitable mistakes like stoopid hooomans, but DO engage in exploitable bug behavior left there by the programmer/s). Neural nets don't get their bugs from the programmer, but still can pick up "bad habits" based on the data sets (a neural net isn't inherently racist, but since most data sets are composed of scraped photos from databases primarily used by white people AND average white person more likely to own a digital camera... data set basically become racist by accident). In the case of poker, since AI never had to worry about paying the mortgage next Tuesday, it would never bother "learning" to play at 110%, it skipped right to 157% (if you follow the metaphor); so bluffing against it became a kind of pointless exercise for the above average player, let alone the average player (plus no body language, etc.).
EDIT: Thinking about this further, my above suggestion about having both sides contract for retreat purposes might be too difficult to elegantly implement (both literally and for AI decisions to exercise). Prolly easier to just allow direct retreating from any other side of map after some time period that varies depending on the total DP/fleet size of entire battle (like maybe only 10 minutes for a small battle, but 20ish for a large battle), BUT the tradeoff is that while direct retreat will always choose the most direct route to any map side, if ship ends up retreating from any side of the map that isn't that fleet's starting side, ship takes some CR and hull damage (even more if the hostile fleet side is the closest retreat side). But this would only be the case when using the direct retreat command, while tactical retreat command would still just retreat normally to the fleet entry side (ie, retreating from that fleet's entry side is free, no CR penalty or hull damage; thus sometimes directly retreating is still free, so long as direct retreat command given to a ship that is near proper retreat side). This would be only in the case of normal battles, pursuit battles would stay normal (ie, pursuit battles still have to make it to the far side of the map in order for any given ship to "escape," while avoiding enemy ships that pop out of sides). I also can't remember if the game already did this and then it got dropped; if so, please disregard.