Several things...more of AI issues than bugs...that I've noticed during my first ToA game...

Terrans, Tough, default map size and options, no random intel, no map regens, tech trading disabled since IMO it's always been broken, so AI not reduced per se, but no tech trading seems to affect the AIs them since they can't do team research.

I'm playing Terrans and at peace with everyone.  Most everyone else is at war with 1-3 other except 1 AI who's so cornered he might not have contact with enough warmongers.  Arceans (sp) are beating up Altair who surrender to me (for no particular reason).  So I take control of the Altair planets that are surrounded by Arcean ships.

Issue 1:  It's been at least 30 turns, Arceans are at war with 2 other factions, and the ships they had at Altair have never moved even though "their territory" is getting flooded with invaders.  It's like those ships had a goal of beating up Altair, which has become my planet, and since we're at peace and they can't attack, they just sit there, frozen in time for all of eternity, stunned by getting dissed.  I doubt they're considering attack me because my military power is considerably higher than anyone else (this seems to matter) and we're "close" (relations don't seem to matter much).

Issue 2:  Why would Altair surrender at all when the Arceans don't have a single transport in their entire navy (and might not even have planetary invasion tech)?  Not to mention they're at war with 2 other factions and not fully dedicated to Altair only.  Ie, why surrender when your planets can't be conquered or damaged.  Makes zero sense.  Actually, I've yet to see a single transport from any AI yet - they're all engaged in near pointless wars of terror on each other.  I'd imagine all they're doing is crushing their econs and slowing their teching.

Issue 3:  What's the point in AIs going to war without transports?  They can beat up starbases and harass each other but it's ultimately fairly pointless.  AIs should go to war for a good reason (or due to diplo pressure, or superability manipulations).  I doubt they all bribed each other into these wars - the racial makeup of the galaxy wouldn't seem to lean that way, and I as Terrans and master diplo only caused 1 war long after the initial onslaught.  Either way, no wars have ended - just more wars piling on.  I mean, if you're coerced into a pointless war you might end it asap rather than wasting resources on it.

Issue 4:  (opinion) I dislike how an AI will "surrender" to some random party when it's getting wailed on.  This time I got 2 planets randomly but usually it's me beating up an AI and them surrending to someone else.  I think I used to disable this in DL (and will look into it again for ToA).

Issue 5:  The Yor built two influence bases in "my territory" that are so far from its border with me and that are so far out of the way that there is absolutely no chance of them ever doing anything except irritating me.  Yo, dude, I'm the Terrans and my influence is overruning your home planet - your influence bases won't even affect the pixel they sit on.  I don't think they could be just to extend range either as they're near each other and near the (dead, no resources, no remaining colonizable (even harsh environ) planets, but swamped in my influence) corner of the map. 

Meanwhile, two of my planets (same system) were close to the Yor homeworld and quickly had influence problems (early in the game) so I built an influence base near them and eventually pushed influence to keep them safe (and eventually put their homeworld in jeopardy).  Had the Yor put ITS 2 influence bases in opposition of mine, it might've flipped the planets or tried - ie, done something useful with them.

Issue 6:  I attacked the Yor due to those annoying star bases, took their home planet (another pet peeve of mine - building bases in my territory is like begging to be slaughtered), which wiped their influence, and evnetually their mini planet revolted or something and the Yor surrendered to me (or that's how it appeared - planet mighta flipped).  It seems odd that a races' last planet can be flipped.  Seems like they'd hold out til the bitter end no matter how much influence they're getting swamped with.  But, I didn't mind, since I was out of transports.