Some of the highlights seem to persist, even when there isn't any hive present.

Normally the highlight disappears after the skirmish has been successfully completed, so I think this is caused by eliminating the hive before allied forces have been assigned.

Can you give an example of where and when this happened? And would logging out and back in fix it?

There are a couple sectors that I can't really remember off hand, I think Odia O-9 is one. Logging out and back in doesn't fix it, other players can see them too.

Here's a video:
https://youtu.be/BYWNWLD7hPQ

this morning, the sedina map showed two levi skirms ...D-3 (actual) and L-14 (empty)

Thanks. I think we found the problem. It should be fixed in the next server restart.