Fairly certain this always happens to Kaidan and EDI, it's like the Barrier and Defense Matrix get deactivated, which starts their cooldown. Also happened in original ME3. The only way around it AFAIK is to not level up those powers for them at all.
We need a more detailed option for M3, like in the first ME, where you can choose between full manual control, defense only or fully auto Squad powers in the gameplay options.
Somehow I doubt this going to happen, or what do you think @holger1405 ?
Not sure about ME2, but squad powers off does not seem to activate defense powers there. At least I never noticed it there.
Then again I almost only use Miranda and Garrus in my current playtrhrough, but having loyal Grunt during Mordins loyalty mission with me, I didn't notice him to auto activate fortification. Ammo powers are automatically selected, though.
I think if Bioware wanted to streamline this they would have done it before releasing the game, so I doubt that they will do it now.
Personally I also would like offensive and defensive powers to be separated in the settings. I always shut down the offensive power use in ME1 and have no choice as to shut it down completely in ME2 and 3 because I want to control the offensive power use of the squamates myself.
For the Bug, it is exactly as @szaumoor said, it is a problem that is related to EDI and probably her "Defense Matrix" power.
(Can't say anything about Kaidan because he never made it off Virmire in any of my playthroughs. 👿 )
I have everything on manual, the bug still happens.
I like having all the control, especially that I tend to play on Insanity - that's why things like this drive me totally nuts. Or e.g. the fact that there is no "aim assist off" option in the game (Xbox version). Settings are abnormally useless in MELE.
This happens to all squad members using armor that can be somehow purged. Not only Edi, James and Kaidan, but also Wrex, Grunt and Jacob. On Insanity, this is a huge drawback as the beginning of a battle often has to be quickly dealt with in order not be be overwhelmed by enemy forces.
