No weapons when they went to see engineer?

They did bring weapons, just not on either of the first two trips because Shaw refused to allow it. The mercenary, the only one left after Fifield's attack I'm guessing, that was present at the Engineer's awakening had a weapon but only managed to get one or two shots off before the Engineer threw him across the room.

Jackson had a shotgun.

I too saw a person with a shotgun..

There were two Mercs which seem to have just disappeared they had guns! A major problem with this movie for me was that nobody was really in charge outside of the ship. Shaw decides not to take weapons. Milburn and Fifleld just decide to leg it at the first sign of trouble or boredom. There seemed to be a serious lack of seriousness from a security point of view.

They did pump him full of lead. Someone fired a shotgun at him twice.