Normal:
Weird:
Hello. ~~~~ P.S. Also this other thing. ~~~~
It makes sense -- that'll get parsed as multiple comments, and the way the highlighter works is that it's passed the ID of the comment you replied to and it highlights the most-recent comment that's responding to it. Technically this doesn't even have to be your comment, though you'd need incredibly implausible timing to ever see someone else's comment highlighted.
We could probably fix this most-thoroughly by changing the DiscussionToolsEdit:addcomment API so it does a full parse of the new wikitext and returns any new comment IDs that're created, then change the highlighter so it would accept that. That's more expensive, though, and this is an incredibly niche problem.
Alternately, and cheaper, we could maybe alter the highlighter so it'll highlight the most recent comment and all other comments with the same timestamp?