If you're talking about how there's a log entry for normals and an entry for heroics, that's always been the case. Other than that, all I'm seeing are logs where it looked like the log was cancelled and restarted in the middle of a raid, resulting in another set of logs.
Edit: For today's logs, I'm seeing two entries:
If that's what you're seeing, then it's perfectly normal. If you had done zero bosses on heroic, you'd just see the first line. If you'd done zero bosses on normal, you'd just see the second line. Since you're doing a mix, you'll see both lines.
21:18 Throne of Thunder 10N
Throne of Thunder 10H
Does that help?
If you want an example of this effect, look up the logs of some of the top guilds. I used Midwinter, since they're on my server. Most of their main raids just display the "Throne of Thunder 25H" line. I see one, however, that has both the "Throne of Thunder 25H" and "Throne of Thunder 25N" lines. That one shows a single wipe to Jin'rokh (which means they accidentally pulled on normal mode). I also see another one for their GDKP run, in which they kill heroic Jin'rohk and the rest on normal. Once again, that raid has two entries, one for normal and one for heroic.
In other words, what you are seeing is exactly what happens to every guild that uses WoL. It's been this way, afaik, since WotLK. Definitely since Cataclysm.