Yea, CPAs don't care about the strength of the unit, they just release what's available, on a one-for-one basis (partly because otherwise the CPA announcement would be made a liar: it doesn't know which ships will be available at launch-time, and it's already given you a literal number). The AI did "pay more" to get those low-cap ships in the first place, though; whether it was from initial-spawns, initial-barracks, or reinforcements.
Also, it processes each planet in turn, and releases all the ships there it can (of the tech level that it's trying for at the time), rather than going for maximal spread-across-planets. Therefore, if the order of planet processing happens to pick more planets that have low-cap ships as 1 or more of their 3 "focus types" (for reinforcements), they'll probably release a lot of those.
That said, I don't dismiss concerns about the-AI-getting-low-cap-ship-for-same-cost-as-normal-cap-ship out of hand, but I do need details of what exactly happened (saves are good), and proof (logs are good) of it happening. Otherwise I'm kinda shooting in the dark to figure out if it's actually a bug, or just a perception.