I took out one AI about 90 minutes ago game-time, but I haven't seen anything at all coming out of it's exo-galaxy wormhole.
Given it was previously spitting out one to two starships along with a few dozen other IV ships per disgorgement, it seems kinda strange I haven't seen anything.
EDIT: And on that note, I just saw the yellow AI's core command center spawn 250 of the pink AI's ships. The pink AI is the one I've already toasted. Err, wha?
This is all working as expected. Exo-Galaxy wormholes don't allow for reinforcement, they only allow for offensive waves. So the reinforcements you were seeing were actually coming from the AI Command station, which you destroyed. Having an Exo-Galaxy wormhole on a planet you captured is the same as having one on your starting planet from the Backdoor hacker. I played with that over the weekend, and it seems to be working fine.
As for the "dead" AI still spawning ships on the yellow AI's planets (or its own for that matter), that is also by design. The AIs don't get hampered at all by you destroying their first command station (in fact, they get a boost of 100 AI Progress). It's not until you destroy both that the game is won or lost. This holds true for human players, as well. When one player loses their home, if other teammates still have home planets, play continues as normal. It causes some AI progress boost there, too, and also causes a loss of some income for the player who lost their home planet, but no players, AI or human, are "out" until the game is completely over.
This is a major selling point for co-op players, and it also prevents that "it's all downhill from here" feeling that you get with the end of a game with many other RTS games. I've seen in a few other threads that you stopped some games near the end when your victory seemed assured, and to that I say: your victory was not assured.
When you take out the first AI, that +100 boost can often swing the victory to the AIs if you are not prepared. A number of people have lost at the last second, with the AI sneaking freed core ships over to the human homeworlds and destroying them, too. Like a cornered animal, the AI is very dangerous right at the end.
Of course, when both the AI planets were being right next to each other, that often meant you could finish off the second AI too quickly for this to be noticable, but now that problem is solved with the AI planets no longer being close together. So, I'd be reluctant to stop early and declare myself the winner, is all I'm saying.