The hole/flaw/bug involves the uninhabited and unplanted asteroids which are "pre-owned" by the AI. If you put some seeds on one of these empty AI planets before the AI gets there or sends any seeds there, but don't plant any trees, and it is the most desirable asteroid in the AI's expansion path, the AI will completely avoid that asteroid or even cease expanding completely. After noticing it in Infinity, I played through Infected Empire a few times and was able to induce the same buggy AI behavior there as well.
Before detailing the AI problem I want to describe my strategy for winning this level since I discovered the flaw while developing it
The early phase of my victory strategy for Infinity is to get the seed economy going as efficiently as possible and also quickly capture the two upper-most asteroids in the home quadrant so you can put about 45-50 seedlings on the first comet that swings by. That is usually close to all my seeds at that point of the game, but if you have taken those two top planets, and fully planted the first three, you will quickly grow enough to conquer the remaining two asteroids with plenty of time to build a large enough force to crush the first invasion when it arrives. One seedling from the first comet gets transferred to the other comet so I can orbit it around the upper right quadrant's sun in order to get an early look at the AI's base and how many seeds are coming on the invasion comet. The remaining seeds ride to the lower left quadrant for an early pre-emptive strike to cripple the AI there so I can get those asteroids producing seedlings for me instead of the bad guys.
After the first run through with this strategy, it seemed quickly winning the lower left wasn't quite enough to guarantee victory as the AI kept hammering me with huge invasion forces from the upper left. Next game, I let a bunch of seedlings stay on the first comet all the way to the upper left to get an early peek at the AI stronghold. I was surprised to see most of the asteroids were still empty at that early stage as the AI was still in expansion mode. I hopped all of my seedlings onto the empty corner asteroid (the one closest to that quadrant's sun planet) and planted a tree. This slowed the AI down appreciably but didn't quite do enough I thought.
The next time I tried this variation of my strategy, after landing my seedlings on the upper-left corner asteroid (owned by the AI but unplanted), the game wouldn't let me plant a tree even though I had enough seeds (a bug in Eufloria itself). [aside--this game bug occurs sometimes when you have this exact situation, friendly seeds on a virgin enemy asteroid that has neither trees nor exposed roots but can be planted. Effectively you cannot select the asteroid--the asteroid menu with the tree buttons disappears when you release the mouse click after selecting the asteroid, making it impossible to click the tree buttons. It seems to only happen with certain numbers of seedlings on the asteroid, above which it doesn't occur. This bug is entirely separate from the AI bug but I mention it in case Alex or Rudolf are reading, and because the one led me to discover the other]
Anyway, this was a frustrating situation--I had sent ten of my precious seedlings deep into enemy territory on an important sacrifice mission but they were suddenly stuck in limbo. I couldn't plant a tree and I also couldn't retreat since there were no adjacent friendly or neutral asteroids But here's the AI flaw--surprisingly, the AI completely avoided that asteroid like the plague! The AI kept developing the other asteroids in that quadrant, but would not touch the corner with my lowly ten seedlings on it even after having the maximum 100 seeds on each of the other planets. It also _never_ sent seedlings onto comets as they passed by even though the comet's path in that quadrant brings it within the send radius of the two next inner-most asteroids. Needless to say, eliminating the threat from the AI's strongest forces with only a handful of seedlings made the level something of a cakewalk
A little more detail on the bug: After mopping up the AI in the upper right, I sent about 2000 seedlings to that corner asteroid in the upper left. With no trees planted, the AI still stood in place. The instant I planted a tree, the AI finally sprung into action and ran into a deathtrap. I tested the bug a few more times with different numbers of seedlings. When I put only one seedling on the corner, the AI invaded like normal. With seven or more, it wouldn't invade. However, when I also put seedlings on the asteroid directly above the corner one, the AI invaded normally.
That dovetails with what I saw in Infected Empire. First I cornered the AI on one asteroid, carefully leaving a trail of open virgin enemy asteroids for the AI to expand into, some with my seedlings on them, some not. When I had seedlings on the one biggest asteroid within the AI's occupied asteroid's send radius, but didn't plant a tree, the AI wouldn't expand. The AI wouldn't even expand into other reachable unplanted AI asteroids that were completely empty. So long as I kept my seeds on that one best asteroid within its reach, but didn't plant a tree, the AI wouldn't expand. However, if I planted a tree on one of those other previously empty, less attractive asteroids that the AI had ignored earlier, it attacked.