I just started mapping like two weeks ago and for some reason there were second level regions in my country (Monte Dorado) that I haven’t been able to figure out how to completely delete.

They don’t seem to show up on the map anymore, but they are still visible in JOSM which causes me a headache when trying to plan the new internal borders. For example, you can see two of them in JOSM at 33.39 S 40.92 E. Whenever I try to delete these (and other internal borders) JOSM throws a few errors and refuses to upload the change.