I thought I was just imagining it.
No, TF2's hit detection with hitscan weapons is awful (it doesn't bother me if I get the kill but if it's the reason I die then it annoys me.) The only things that can reliably do damage are projectile based ones. Hell, even melee, fire, Jarate, and Mad Milk aren't reliable, I've had Jarate land on someone's head and it not count, it's rare, but it happens. I hope the new source engine has better hit detection, that is the top of the list on my wish list of things for Source 2 to have.