Yeah, I posted a quote that states that if you're in an encounter zone and got spotted the enemy and companion AI will act weird. You'd have to perfect stealth (meaning you can't get detected at all) an entire encounter zone to avoid shyt like that from happening.
It might be glitches. I just cleared the Hotel. Something weird happened when I got up to the the third floor there were three Hunters talking and once I come up close behind a shelf they decide to separate and search rooms. One heads my way so I fall back to use the rooms I came from for cover. Once the Hunter closest to me is isolated I stealth choke him and for some reason the rest knows I took him out and start running around searching for me
Ellie was with me the whole time, the first guy that came through Ellie threw brick at him to stun him and I take him out with an arrow. I waited for the rest to come up and maneuver to stealth choke the others that got close to my hiding spot.
There was one last dude that was searching for me a floor below but then I couldn't find him with listen mode after taking out the others. I looked around for him a bit but then I got tired of it and decided to head to the elevator and move on to the next area. As soon as I used the prompt I hear "motherfukker!" and two more enemy AI rush up to shoot me