I've been puzzling around a bit, and have been able to recreate it, and better understand it. We need two maps, map-A and map-B, and each map has a number of external tilesets, say map-A has set-A. And map-B has set-B.
If only map-A is opened, it just shows the set-A tileset belonging to map-A. When map-B is opened as well, the bug occurs: map-A now also shows the external tilesets set-B. And map-B shows the tileset from map-A.
In the picture from my above post, I indeed have multiple map-files opened, so the extra tabs must be the result from those tilesets also being imported in the other map files.
So put together: have multiple map files open, which have external tilesets. The external tilesets from each opened map also show in other opened map files.