This happens whenever a story is changing rapidly. It doesn't have to do with merging the threads—it has to do with different comments dating from when different information was available. In this case the initial story was "might acquire" and then turned into "has acquired". The threads weren't neatly partitioned before we merged them; people just post to whichever discussion they happen to see.
When a story has been changing while the comments have been accumulating, HN readers are smart enough to figure it out, and I'm not sure adding new software would help much.