If you think your players are mowing down the enemies too easily, make enviroment THE enemy. Use toxins in form of gas in whole complex. Let them be bombarded with hard radiation (effects of Cataclysmus device from Lathe Worlds online supplemet). Let them fight in vicious storm (-30 on BS). Roll for random psychic phenomena regulary on haunted place.

That is what I learned from Arkham Horror. Yeah monsters, yeah coming doom, whatever. But when your surroundings are againts you, than you realise the gravity of your situation. 

 I've run into this problem many times myself actually.  I used to play with a alot of current and former military being former military myself.  The best strategy I can give for the GM is an old saying we used to have.  "Everybody has a plan till they get punched in the face."  No matter how much time anyone plans on anything to happen something can and will go wrong.

The perfect example of this if Final Sanction.  The original mission the player have before everything goes south is actually pretty easy.  The just waltz into Landsholm with an Inquisitor and her full group with PDF support and burn the xenos out.  From the off set everything goes wrong.  The cruiser gets pwn'd by some Krakens and the team has to make landfall in drop pods in an emergency.  When they land they find a planet full on in genestealer-driven rebellion, no inquisitor to be found and the PDF scattered all over the city fighting for their lives.

Planning is good and having military people playing Space marines adds a lot of versimilitude to a game.  Deathwatch is not a game on the other hand where anything is normal.  Even in the real world missions despite planning can go wrong.  Intelligence is not an exact science and can be wrong a lot of the time.  Aliens bring with them strange tactical considerations into a game that cannot always be accounted for.

Using Bad intel all the time can be heavy handed and will make the characters not trust any intel in the game period.  But not giving the players a clear picture messes with their planning.  I imagine that the players superior planning is your big issue here.  Try taking the players out of their element every so often and giving them challenges that they cannot plan for makes for exciting game play.

Hope this helps.  Game on!

 You could also use enemies that use superior planning in their tactics.  Enemies occupying the high ground surrounded by a terrain feature that is hard to get too (mines, lava, canyon).  Trench warfare is a good way too, making every piece of ground hard fought.  Terrain and environment is great like the above poster stated, adds a lot of drama.  When PCs overcome these odds too they feel a real sense of accomplishment.  Eliminating player options on how to proceed to an objective changes things drastically.  Instead of giving them 3-4 options give 1-2.

 Make your players Ammo count -  really accurately.

Then introduce a horde.  A BIG one.

Practice your evil laugh, for when they start running.

Huros said:

I'm hard pressed to think of a horde that will stand up to 60 rounds of heavy bolter metal storm ammo, let alone 250. Also beware of flamers and the talents cleanse and purify and storm of iron. No horde of a sane magnitude (Less than 150) will stand up to that for very long. A kill-team equipped to deal with hordes will fight a lot of curb stomp battles.

Penpen said:

Indeed they will. However a kill team will often have to battle through thousands of enemies to complete there objectives, and potentially the same again if they go hardcore on all secondary and tertiary objectives or are just glory hogs.