I'm guessing that this is a pretty fundamental problem that's been overlooked. I've never seen an AI try to Capture before, and I'll bet they're borked because all of the nearby build-spots are "covered" with "units". Poor things, they're too stupid to realize they've been given a fortune in new resources and ways to hose players, especially players who don't bother scouting

What to do about this?
Well, I think that AIs need to either attempt to Capture the Gaia units, suck them up as free resources, or kill them, by force-firing on them. They shouldn't kill things that don't attack them first, however- they should probably capture them, since they're going to always be too dumb to know what Gaia stuff is a nifty tech upgrade, and what's just some free lunch. But the days of "that's a tree, go get some E" are going to be over. Very, very soon.
Not having AIs make this fundamental choice will cripple them as I get my new LUA code, that very heavily makes use of Gaia, in play, and mappers / modders start using it.
I'm going to have a tech demo ready sometime fairly soon, and it's going to show you what the future looks like- I haven't been this excited since the early days with CEGs, let's put it that way... this is going to change everything about how we interact with maps, both as game designers and as players. AIs need to adjust, too.