The tile map is programmatically generated. When a new map was loaded, I was destroying the render data and re-creating it before setting the tiles in the different layers. Maybe something is has changed in the way I should do this. Basically, I was doing the following:
// map is tk2dTileMap
DestroyImmediate(map.renderData);
map.renderData = null;
map.Layers = null;
tk2dRuntime.TileMap.BuilderUtil.InitDataStore(map);
// loop though the map and create the tiles
..looping code...
map.Layers[0].SetTile(x,y,tile);
map.Layers[1].SetTile(x,y,tile2);
map.Layers[2].SetTile(x,y,tile3);
map.Layers[3].SetTile(x,y,tile4);
..end loop
map.Build();
When I don't destroy the render data and re-create it, I get pre-fabs left over from the previous map.
Basically, I need to reset the map to be "empty" again, including prefabs, and then re-populate it. Maybe there's a better/different way to accomplish this.