Seems like AIs pay too little for low cap ships. (Especially for Starships in Exos)
What and how many ships did the CPA have in addition to the SSBs?
Except for exos (which are known to be a bit...off in terms of cost balance), do you have any evidance for that, or just a "feeling"? (Keep in mind, number on one planet does not count, rate is what matters, do they get more than they seem to be able to reasonably "pay" for per given amount of time). From what I have seen, waves, reinforcements, and special forces' math seem to be working properly.
I have mentioned in the past that I do think one factor not put into consideration for the AI "costs" is build time and resource costs (the AI can pop out a SSB and its equivalent "cost" in laser gattlings in the same amount of time, even though there would be a good chance, for humans, it would likely take you longer to get that SSB out), but that only really matters in the short, and to a lesser extent, mid-term. In the long term, any skew by initial build time and costs begins to fade in terms of importance (provided you can keep them alive!), so I don't think it is that huge of a deal (unless you like to play more aggressively and faster, in which case, the AI being able to reinforce low caps at the same rate as the "equivalent" number of high caps, while you very well might not be able to, could start becoming noticeable).
I will say though, now that the "preferred ships for defense" per planet logic, there is an increased chance that the AI will build up a near un-counterable number of low cap ships on any one planet (yes, this can happen with high cap ships too, but generally, it takes much more, even if you scale based on the cap differences, to reach that point for high cap ships than low cap ones), so I wonder if the "ultra low" cap ships need a "max per planet" logic reinstated for them, now that the anomalous "skew" for them is now much more possible.
Basically, this may very well be a problem with some of the low cap ships themselves and/or some of the high cap ships. Like if a low cap ship has 1/20 the cap of the "standard" cap, but has, say, a single of that low cap has 24x the strength of a single of one of those mid cap ships (thus making a cap of that high cap ship 1.2x as good as the mid cap ship cap), then of course a ship cap ratio based cost will be off, because the stats themselves are even given their caps (aka, that lower cap ship is OP even given its low cap).
Finally, for starships, ever since their buff, I do think that at least reviewing how the math for how the AI gets them in waves deserves at least a lookover.