Scout more often and keep an eye out for "back door" attacks?

Maybe you went after the wrong opponent?

If you're playing Entrenchment or Diplomacy, perhaps strong starbases supported by a small fleet would help?

The other thing I wonder, is, whether you're playing Unlocked Teams or with Locked Teams.  With Unlocked Teams the AI will eventually ally with one another and gang up on you, often making it impossible tow in.  With Locked teams, the AIs will always be hostile to one another.  (Maybe it works a little differently in the Diplomacy expansion.)

If you ever venture online and play PvP against human opponents, most games are played with locked teams and a 1-to-1 ally-to-enemy ratio, so it's harder to get doubled than if you're fighting 9 AIs alone.  (It can still happen, and often does happen depending on starting positions, but not as much as if you're alone fighting 9 AIs.)

<Edit> Since you're dealing with AI, it might be possible to distract the second AI with a small marauding fleet.  Scout the enemy on your back side and if you see it gearing up to attack you, have the marauding fleet start attacking its planets and maybe you can pull its attack fleet back and trick it into chasing your small fleet around.

I actually find locked teams worse in diplomacy than unlocked teams. If they are locked they will keep banging on your choke points over and over. If they are unlocked while the opening 30-45 mins (at least for cruel AIs) will be hellish, one of them will get distracted and go elsewhere giving you time to breathe and grow econ. On the other hand I have had unlocked games where I get doubled (or even tripled on two fronts) quickly and those are a barrel full of monkeys. I guess I am saying it varies from game to game.

The AI takes it's time dropping your planets, an advance through your empire gives you lots of room to breath.  Set up a new defensive perimeter one or two jumps in from where you're losing it, and go all out with tactical slots.  4-6 repair bays, a couple hangars filled with fighters, and the rest in turrets, all in a loose cluster at the forward point.

Position your fleet ready to jump into those defensive lines and wait for the enemy to engage before going in.  Make sure to move within repair bay range and keep your repair bays back behind the turrets, not even with them.  Less ships will target them that way.  If you can lose a 250 ship fleet you're pretty well boned already, but this is the biggest advantage you're going to get.

If this is entrenchment or diplomacy, meh.  Max out starbases, nuke the enemy fleet in range of one.