…To try and harm your PCs?

I've been running Broken Chains with my group and is actually the first time I've properly GM'ed a game. I mixed things up a bit more since the group consists of three Chaos Space Marines and only a single (surprisingly tough) Human.

The Carrion were pretty useless and the only damage they took prior to the Sanctum Gate was A) Getting struck by a falling gantry and slamming into the floor of the Bilge and B) A Carrion getting lucky with throwing a piece of debris as they were ascending (Agility) and sending another PC falling. At the same time I didn't mind this because hey they're malnourished, weak, underestimating vermin.

Then Crane launched his Acolyte ambush and even though the whole team of about seven was totting Hellgun- errr, Hotshot Lasguns not a single bit of damage was inflicted and at most a bit of paint got scratched off their armour. Queue running in fear. When it comes to the confrontation with Crane I want it to feel like a pretty dangerous and important battle, but how would you propose doing this without it ending up everybody wading through the Acolytes like The Blob? I was considering slapping some Melta or Plasma Guns on a few of them, but at the same time I don't want all of them to be smoking heaps of ash before the end of their first adventure (afterwards on the other hand…)

Oh, and if a turn goes by that the Sorcerer's Doombolts haven't killed somebody something is seriously wrong. Do the rest of the group match his ability as they level up? Our Champion and Chosen are a feeling a bit… left out when Storm Troopers and Carrion are going up in purple flames left, right and centre.

Just curious how you add more threat to your adventures.

personally havent had this problem, but i have heard of others using hordes of 'guardsmen' with some special or heavy weaponry mixed in. or in this case, hordes of the combat servitors could work too

My players for Broken Chains took far too long to get past the Sanctum Gate, so I had Crane and company go after them first. They seized control of the ship's servitor population, consolidated all the murder servitors, and sent them belowdecks to cleanse the heretics.

A Magnitude 50 swarm of murder servitors instantly sawed apart the foolishly optimistic Khorne Berserker and nearly killed the Apostate, but she was dragged out of the swarm with major injuries. After fighting a battle of delay-and-fall-back, the servitors were reduced to a Magnitude 10 horde that dispersed and reorganized in the bilges, to harry the PCs again at inconvenient times.

I also had one character volunteer as a daemonhost and show up for the final bridge confrontation, so there was no shortage of challenge for the players.

So yeah. If you're heavy on Chaos Marines, feel free to tweak things a bit.

Not so much with Broken Chains, but my GM was intensely fearful of our potential as a group.
See, most of them ran ToF heavy duty psyker nonsense, and so the combat potential for the group is endless with an unaligned sorcerer, a Tzeentchian sorcerer, and two Hereteks with psy ratings. Then there's me, I'm a Nurgled up renegade that managed to roll a daemon weapon with the Plague Carrier trait and enough toughness/wounds to take some serious damage.

We, with just the few of us, can annihilate hordes of 80+, we ran tests to prove it.

So, my GM had me draft an enemy that could stop us cold.

So I essentially made a species native to mire, smilar to a komodo dragon/fungi symbiote, that could produce hallucinogenic spores and had the Regenerative (3) trait. Lots o' wounds, psychically resistant, etc.

When your PC's get overpowered, make something else even more overpowered.

You mentioned that you didn't want to equip the npc or baddies with heavy or extreme damage causing weapons but for my games this is exactly what I had to do. I had to custom make some of the NPCs weapons to do more damage to give the game a real feeling that, Hey I may not survive this encounter. For me this is the fun aspect of the game. Who always wants to not get hit. The way I countered this was giving the weapons felling and proven qualities for ranged weapons. For melee I gave the weapons the razor sharp quality which would effectively give more damage to pen. Remember the golden rule that you are the Game Master and have the final say of your game. If a npc has to have a certain weapon and the damage doesnt seem to match up. Change it. Heck you bought the book.

A sorcerer with Doombolt killing everything? That's not even a particularly good psychic power for killing people. It's hardly better than a Plasma gun assuming you're not pushing (which makes everything risky anyway). High PR Force Storm or a multi-target power with Warp Weapon? That's dangerous.

I'm generally pretty honest with my players, and since they are fairly careful and prudent, they rarely fall in traps or ambushes that would kill them. That isn't to say bad **** never happens to them, just that it isn't too unfair. And I think the best way to handle different damage-soaking abilities is weapons with high penetration and/or felling, or big restrictions (if you stay away from the Khornate Berserker, his Chainaxe won't hurt you). Hordes are a good way as well, as you can easily differentiate their rules depending on PC size (more attacks, dodgeable, without a damage bonus for medium-sized, and the opposite for hulking-sized). Obvious, big damage sponges that aren't the real threat may be an answer too.

However, I generally avoid just rolling the dice to tell them that a lascannon hit them: that's cheap and basically has no interest, rp-wise. Let them know there is a lascannon/bloodthirster/baneblade/eldar autarch/ork nob/whatever you fancy in their way: they either try to take it out, taking risks (in which case they can only blame themselves if something happens), or change their plans, in which case, yay, more rp.

Tldr: yes, put more big-ass stuff in their way, but don't spring it on them by surprise. Unless they just walk into it blind and wilfully.

Agreeing with everything you say, I do think surprising the pc's if I roll an stealth vs opposed awareness test. At least in this method it's justified and while there is no sure method for exacting encounters, I usually go by the method of 1:1 ratio, for less baddies I go 2:1. This way it seems that every player character will have sometime handling his advesary in combat. I think the first encounter in my Only War Eleventh Hour game I adopted eight Ork Kommandos that surprised around seven or eight players. I wanted to adopt a Vietnam feeling on a death world jungle planet and rolled a few concealment with silent move skill tests even though I don't think the skill is offered in the Only War series. The Sarge was killed by Choppa attacks to the leg critically injuring him to the point of dying by blood loss. I actually rolled under the 10% for a character to die and used another choppa attack on the Priest who was heavily injured with 10 wounds. A few shoota attacks against the players as the others took 4 and 1 wound to them. They set a kill zone and overwatch pinning them so they couldnt advance and took them eventually out with semi auto auto cannon attacks. But this is the first encounter. I think surprise is something that has to be rolled by and used at discretion.