Ok, playing around with colors, it seems to me that the refcount is not wrong. However, playlists tend to "lose" their sub-playlists.
For example, my "L" playlist lost all its content. So all the playlists underneath it decreased their ref count by one, and those which went down to refcount=0 generated the error I mentioned previously.

So the problem does not seem to be in the ref count, but in the fact that sometimes sub-playlists are "lost" and need to be relocated where they originally were.