Some ambushes are character targeted, they home in and attack you through any and all stealth. WAI and annoying.
What can help is Placate the big bad as soon as he comes into view, run, and the remaining mobs follow you. Defeat them then go back for the boss.
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Eislor has it exactly right. Now there are some ambushes that are area specific only.. they respond to a spot on the map and will attack anything they find there. I have moved my stalker through a doorway and stood and watched each ambush arrive and stand around waiting for me to AMBUSH them. Others ambushes will hunt you down no matter what and because of THAT see right through your stealth. Its not a bug its WAI.
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Cool, thanks for the reply. I will try PL and running. Stalkers are such cowards. 
Here is my question or rant.
I have a 31 stalker and he pretty much kicks butt, at least to me. So I am doing a mission, "Offer Artifacts to Power", CoT. So I get in there, clear the room, touch the alter, and bam here comes the ambush. I fend off the first 2 waves no problem. The 3rd group has the big purple Boss that flattens me in a few hits. The problem I have is that I was hidden when he attacked me. So, I died, went to the hosp. I went back, hidden of course, he did not see me this time, so I AS and he was down in 3 hits.
So my question is: Is this a bug? I would think that I could at least have a chance that an ambush would not see me. He seems that an ambush situation is programed to just attack you regardless of you stealthiness.
Any thoughts? Thanks!