This is a screencap of my map in QGIS:
Those orange bits in the middle of each section are actually holes in the GeoJSON file and I can't make them go away. I've tried using the "Vertex tool" to select the vertices and delete them with "Delete ring" but it doesn't seem to work.
How can I cover them?
DeleteKey. If you have problems with the merge function, you should try the Repair Geometries tool from the Processing toolbox.