Seems the AI is ignoring some high damage attacks and leaving it's shields down when it has the flux to keep it up.
For example, I recently found an Apogee (never used them before) and was playing with different loadouts in the combat simulator. I sent it against the two Sunder's on the opponents roster.
Things were ok for a while, but then while my AI controlled Apogee focused on one Sunder (the Autopulse laser version); the AI thought to drop the shields, ignoring the other Sunder with the High intensity laser frying my left flank.
It was almost like the second Sunder wasn't there; and the damage didn't register with my AI controlled Apogee (it didn't try to turn to avoid further damage in that region). I was under half flux at the time, so there was no reason to drop the shields then.
I've noticed strange behaviour like this elsewhere with different ships. For example in a real battle, I found my Tempest ignoring the huge damage being done to it by another ship to focus on something else.
I also tried the Aurora earlier on today and found similar behaviour with the AI dropping the shields at reasonably low flux levels and taking heavy damage that could of been avoided by leaving the shields up.
You can see this pretty easily, just loadout another Aurora yourself and start the combat simulator selecting the Aurora on the opponents roster. In this case the shield was being switched off with a solitary opponent and as a result, quite a few shots from the Heavy blaster get absorbed by the hull that could of easily been absorbed by the shield.
EDIT: Sorry, I forgot to mention that there was no officer on board (ie the slot was empty, just the normal AI)