why do some people say "having said that" during conversation?
The speaker , for example, already talk about an issue during discourse. why would he/she need to say "having said that" ?
Is it proper to use this phrase?
It's a fine phrase to use, yes. It's synonymous with that said:
English is a very difficult language. That said, there are many opportunities to learn English since it is spoken all over the world.
That said, means (to me), "While that (the preceeding is true) the converse (which follows) is also true;"
Or "While accepting the aftorementioned, it is also true that,"
The following may not directly contradict but at least qualify the aforementioned.
It is very similar in meaning to "That being said," which is a little more formal and perhaps a touch softer in the extent of the contradiction that it introduces.