i've noticed this problem on the web interface as well. i've noticed it after clicking the "load more comments" button.
someday it might be good for pumpa to sort comments by time, unless they are intentionally being sorted some other way.
i looked at an old thread in pumpa and saw that two comments in an older thread were swapped. it ought to be in your meanwhile feed in pumpa.
i restarted pumpa to see if that would resolve the issue, but now pumpa doesn’t display the first message, and doesn’t show a button to load more comments. the original 2nd and 3rd posts are still swapped.
Sazius: Yeah, unfortunately Pumpa is unable to fetch the rest of the conversation if only a reply is in the meanwhile feed. There’s a bug report about this: https://github.com/e14n/pump.io/issues/873. Pumpa does its best to collect what it sees in the feeds to the conversation. In my case I see only the original post (because it was included as inReplyTo object to cwebber’s comment (which was in my feed). Then I see your “It’s a joke” reply, since cwebber favourited it causing it to show up in the feed.
With regard to the ordering, I’m wondering if people liking the posts later might be confuse it? Not sure…