Indeed. I have have thrown stuff at the wall when this happens, it is hard to control. There is nothing worse than seeing a clean enemy, pumping a clip into him, seeing 5-8 different blood spots all over him and the game telling me I hit him once, or twice for 30. Sometimes even not hitting him at all.
Overall, the poor shot registry is due to something within the source engine. It is truly unfortunate considering I LOVE all of the games, but I don't know if I have ever played another game where you shoot someone and they don't die.
Happens in CSS all the time also, especially frustrating in competitive play. In CSS at least, some of the problem can be fixed server side. But even a $80 11-slot private server sometimes doesn't register all the bullets.
In the end, Valve needs to revise their product, but then again they seem to be incredibly slow at this. I wouldn't expect to see an update until they come out with a new engine.