Okay, I loaded your save Wingflier and here's what I saw. (I cheated significantly to survive this, that's a seriously nasty setup you have there.)
Time stamps are from the time I warp forces into the AI Homeworld and I'm only showing the CPA post, the Raid Engine post was behaving as expected.
00:00 First CPA Wave gets released, about 2400 ships.
13:50 Second CPA Wave gets released, 46 ships.
When I say released, I mean the CPA is loosed and the threat meter jumps. At no time do any of the CPA waves show up in the wave warning box, they just happen.
You can see the countdown to the next wave on the guard post itself, but not in the wave warning box.
There is a small silver lining in that because it does not go into the wave warning box, once the CPA guard post is destroyed, no more CPA's get loosed at all.
Reading the description of the guard post, I'm not sure these are bugged. It looks like they just trigger a CPA every 13 minutes and based on the huge number freed, I would expect you would get a CPA anyway reasonably soon. (Note the immediately in the guard post description.)
With the second wave only being 46 ships, it does not look like the AI gets to warp in any extra ships for the CPA, if you can somehow weather the giant threat spike of the first CPA, the follow up ones should be tiny in comparison.
You can still make a case for this being unbalanced I think, but from what I see I don't think there is a bug affecting your game.
D.