The single most frustrating thing for me about Discourse is when I’m catching up on a long thread, and I see a comment I want to reply to. So I quote the text and type my short reply.
Now Discourse jumps me to the bottom of the thread, and it’s incredibly frustrating to try to find my original place to continue reading. Combined with the flat nature of the discussions, this highly disincentives me from participating in long threads. Mailing lists are better at this.
5 years later and this one is still the most annoying thing about Discourse for me 
Apologies for the resurrection rant!
How are you using discourse? This does not happen for me.
“Normally” I guess? 
I mean, I’m just using it in a desktop browser, and just use the normal “Reply” (to post), “Reply” (to thread) buttons, along with highlight to quote.
The problem comes in when I have a long thread to catch up on. Say I’m reading message 83 of 147 and want to reply to something in that post. I highlight some text, fill out the text box, and hit “Reply”. Now the upper thread display jumps me to the bottom.
I’ve gotten into the habit in such situations of trying to remember the message number I was on before I hit reply, then after replying, I use the scrollbar to go back to, e.g. 83 to continue reading.
Aha, you mean when actually replying, not just when pressing the Reply post on message 83. I guess you could see this is part of the discourse encouraging you to not spam messages and to just compose one long message.
I didn’t read the whole thread, but it does look like deliberate behavior.