Grenades going through people and disappearing is a glitch, and I believe it's fixed (but a lot of servers are still running old versions).
Shooting people right in front of you is, ironically, probably the most difficult time to shoot them, since the distance they move on screen is the greatest. Several people have posted "nodie" videos, but they've always been a perception issue. I'm not sure what happened in your case. The only case I know of where you can shoot through people is when 2 players spawn in the same location.