It's been a while since I have read the manga but I enjoyed reading it. If I remember correctly, his class was transported to a different world and the God of the world had each person choose their skill, only thing is that once someone takes that skill, its theirs. The main character was transported later than his classmates (I don't remember the exact reason) but he was the last person to choose a skill and all that was left were terrible skills. The God pitied him and let him have all the other skills no one else wanted. He was then transported and as time went on we find out that the skills were more useful than what it appeared to be (A little more information - One of his classmates ends up being corrupted and starts killing his fellow classmates (the delinquents specifically).
I think this is Loner life in another world.
It fits your description:
The protagonist is transported after the whole class because he tried to hide in the ceiling of the classroom. Skills are given out on a "first come, first serve" basis and all the good ones are gone. So the god gives him all the remaining skills, which include one called "Loner", a trait he already had in the previous world (although he does not really life this loner life for a long time).
Later there was one of his classmates who killed / tried to kill some of the others.