Found the issue was Hard Shields. I had always used that in the past but the tooltip in ship builder just stated the base damage reduction. THAT'S why.

Other than having a high counterespionage score and lots of spies for protection (a dozen or more), there isn't much you can do about the random "you were framed" events... except understand that the Darloks are probably the ones doing it (and if the Darloks are not in play, then it is probably the Psilons), so the sooner you rush them and eliminate them, the safer you are. Also, the aliens will be more polite and deferential once you have a strong military... but you usually won't see that happen till late game.

You can "save scum" your way out of it by tricking the RNG to generate a new random number before the "you were framed" event happens. Understand that A) its not a true random result, rather the seed number for the RNG is saved each time and based upon the last random seed B) each time you contact an alien race and propose a new treaty, make a demand or ask for a gift, the game uses the RNG to generate a new random seed.

Thus, for example, you have reloaded your previous auto-saved turn and know that a "you were framed" event is coming up, so instead you contact an alien race and ask for something - and in doing so the RNG generates a new seed number. Save the game again and now when you subsequently end your turn, the random "you were framed"result will hopefully no longer happen. If it does, reload your saved game and contact a different race than before and do it all again (e.g. the RNG generates a 'random' diplomatic response using the previous seed for each race once per turn, but only if/when you initiate it). Repeat as needed.

Combat damage and missile/laser hits also use the RNG, so you can similarly generate new seed numbers by doing different things differently in battle from a previously saved game (e.g. fire and detonate a different number of missiles, shoot down a different number of enemy missiles, take/inflict a different amount of damage before escaping, get shot at by lasers for a different number of combat rounds before the battle ends, etc).

If you don't (or can't) save scum your way out of it, the only answer is to fight the offended aliens to a draw. Eventually if you are winning the war, they will sue for peace.