Weird! I never noticed that.

Indeed, it does!

  cd "$( mktemp -d )"
  mkdir a b c
  touch a/f1 a/f2 a/f3
  cp -r a/ b/
  ls b

Resulting content of directory b on one my FreeBSD machines

  f1      f2      f3

Guess I usually

1. Don’t use cp -r so often, and

2. When I do use cp -r apparently I don’t put a trailing slash

Cause I only ever had problems when trying to use rsync, not when using cp or mv :S