that sort of situ has not happend to me the only thing I can think is that that heros have some + perception powers or you have been hit by a AoE attack as both of these would make you visble to the enemy. 
w00t, its great to see posts about stalkers being underpowered i was worried a nerf was coming.... 
Rock eagle hit the nail on the head, your getting hit by AoEs or somethnig with perception.
You didnt say what build you are but unless you are regen you should get some nice defence powers. Slot them and youll get hit less by AoEs.
As for perception i have played 3 stalkers to at least lvl 15 and there are very few examples of enemies who have it.
One particulalrly annoying example is the guards in the robbery missions. Were you doing those at the time?
I have had this bug happen to me as well, fighting or rather stealthing past several groups a mob of three Marcone for no reason start shooting pistols at me.
The second one was fighting a group of Skulls in a team of 6 the two brutes engaged the mob of 6 I ran round the side and went to AS the red leut at the back and before I could activate AS the entire group aggro'd and faceplanted me. I had done noting but move and had no auras up except my hide.
As far as I know the group had no AoE's as there were no Bone Daddys and the group were only level 9's
It has been noted on the American forums as well althought irregularly.
I've been attacked by enemies whilst my team was fighting them, but mostly because of those longbow soldiers friggin' flamethrowers
As for heroes with +perception, I did my cape mission yesterday and the main hero who's cape I had to pinch could see clean through Hide & Stealth & Superspeed all at once, which annoyed me somewhat to say the least 
That alone wouldnt have been too bad, but all the standard basic longbow soldiers for about 20m in all directions got a ridiculous +perception boost too
I only got to do my assassiny stalkery thing once I'd killed the all the longbow, with great difficulty, in Scrapper mode with the bloody +perception longbows chasing me anywhere I went on the map to rest. And then I only managed to do it once cos I had to placate between the named heroe's attacks and placate didnt work properly because of the +percept boost so the timing was somewhat difficult. Hardest. Fight. Ever. (yet 
)
Yeah there are issues with stalkers hide. Some may have noticed them and some may have not..
I know about AEs and such.. but we were 3 in the group and fighting arachnos, hellions, lost and snakes and stuff.. mostly minions too. the fights werent messy at all, usualy like 3-6 foes. Ive been noticing this since low levels when i started grouping with some sg friends who also made new toons. Most of the groups we encountered only had minions with no ability to AE/cone. They surely had no +perception. They just suddenly started to see me like hidden were off when one in my group attacked them.
Anyway, i wouldnt make a post about it unless im pretty sure about this.. but i could be wrong, who knows. i dont 
/D
Ambush crowds can also see through Stealth, because it's like they come into the mission with you targeted as default. siomtimes I enter a mission and Ambush crowds are expecting me, and this is of course all under Stealth, so I don't think it's a bug per say, and even if it is, I deal with them just fine.
Although I've never had trouble in groups with people firing at my enemies, heck a Stalker should never be initiating the attack anyway, especially in a group.
Ambushes , the old style ambushes from CoV don't actually see through stealth. They just get handed a packet of aggro by the mission. And any creature with aggro on you will ignore stealth when choseing targets.
This also has a habbit of planting MM's as the mobs ignore the pets and hit the main guy.
For the original post: when anyone attacks a mob they activate any deffences they have. Some of these will include +per although thats quite rare.
I do kmow that if a pet [including a mission-given follower] attacks. Then some aggro is dropped on the owner. Which means the mobs now consider you a target and will use mele attacks on you if the other guy is too far away.
Also AS does huge dammage, and so causes a lot of aggro for the stalker. And again , if the party is at range the mobs my well opt to use mele attacks on the nearby stalker rather than do nothing. Even if the guys chucking AOE's have more actual aggro.
And sometimes , I too have been randomly attacked by mobs as I stealthed by. I assume that one is just a bug.
Correct. Ambushes do not by default see through stealth. They DO have you auto-targetted, so I don't quite get how that works, but I have on many occassions got criticals on ambushes - at least until they find me and get a successful hit on me - and completely avoided some. The key is to remember that the AI is stupid, and to attack them first.
I definitely have this problem in team mishes.
There's 2 ways to fight a big mob, both have problems.
Get an Assassin Strike in first. Then the whole mob will turn on you unless your team gets right in straight away to take some aggro.
Stand close and attack after they strike. Run the risk of being spotted for no sensible reason! You're still in hide, why have they spotted you? Your point exactly.
So what I'm saying is yes, I hear ya :P
I would like to confirm, I had the same problem with my stalker.
I move into a group and prepare for an AS on the toughest enemy. My team start to attack, and then, for no reason, I see that some of the enemies are FACING me, and try to hit me (they miss, due to my defenses). I'm still hidden, and if I'm fast, I can hit the proper enemy with my AS. However, a single hit will bring me out of Hide thus ruin the whole thing.
When you move up to a crowd of foes and your hidden, then suddenly someone in your group starts shooting at them and the whole pile of foes turn and shoot you down like you were standing there in plain sight!. ok i know this, its the tard in my group that started shooting at them who faulted. But the point is that should the foes turn and shoot the invisible guy?. just because the foes have discovered a group of villains attacking them how comes they see the stalker who's hidden? It mess up the whole fight for the stalker, without being able to do his "whole entrance show", the build up, Assassinate and then burn a few attacks until Build Up is gone and have like 2-3 corpses at his feet. If he cant do that then the stalker is useless. Might aswell bring a brute instead.
This happend to me every time i were standing near the foes and someone attacked. more then half of them started to attack me while being hidden. And yes i could jump on their heads just a few seconds earlier without their notice.
Also, if a bunch of foes are fighting a group of villains and they have all been damaged by the AEs from the group members. Then a stalker moves up behind one of the foes and pull off an assassination and a few mobs turn to attack the stalker. why is that? I mean the stalker havent touched them, and they are hit by AEs constantly but still they move to attack the stalker. Maybe its to make sure stalkers doesnt get too good in groups being able to hide and assassinate every 10 second? (if thats possible with the reuse timers). But then again, the damage dealing AT should maybe be able to take down a mob every 10 seconds?
This stuff might have been pointed out a few times already on the boards. But just want to make sure it have been put up here. It is annoying and ruin the combat for stalkers.
Having a challanging fight is one thing, having one that bugs out and abnormal stuff happens isnt fun. Its understandable if Hero001 sees you when your standing on his head but im talking about normal white con minions.
I can live with this setback and alter my fighting style to fit the current situation but i feel that this is wrong.
Maybe i just had wrong expectations about stalkers and see that they are what a few people say, a hard AT to play, but if this is suppose to happend they are mostly hard because they're gimped.
Ahh, theres so much whining i managed to write down about only 2 things. Sorry about that. Ill put whine mode to off for a while.
/D