I seem to see such errors quite often in our SVN 1.6 repo. We got these quite a lot while we used to just work on /trunk so I don't think it's due to merge/branching confusion. It seems that a cleup and marking the conflict resolved always works, but it's a little concerning to see errors in your version control system when you're just adding/updating/deleting files.
What causes it?
First of all, cleanup shouldn't be needed to resolve conflicts or tree conflicts. It's only for the rare case that an operation failed halfway through and needs to clean up the locks it left behind.
A tree conflicts happens when you have a change on a file that was also changed by someone else, where one of the changes is a tree operation (file move, rename, add, delete).
The TortoiseSvn documentation describes quite well what happens, and how these conflicts can be resolved