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You're correct Alecain, enemies don't spot your allies. This was made as a design choice that your allies mistakes do not give away your position, an issue Naughty Dog noticed a lot of players complained about. Now of course, players (mostly haters) are complaining about this choice but ah well, you can't please everyone. I was happy they made the choice. It bugs me when trying try sneak behind an enemy to have a dumb AI ally ruin it for you.
I general I'd say I agree 98% with Grandy's post above.
Ellie: I had a slice of ham in my hand. I was going to drop it, so I slapped it hard. It attached itself to the wall