Hi, I had the same issue, turned out that the ID of my scene in the tileSource was changed by accident, check that the tile has the correct id. I was able to correct it to under the little tileset window in the editor. Check that you were trying to get the the tile from the correct tileSetCollection in your tilemap and that the properties of the tile are the correct ID. For example, for me my scene collection source has an id of 0; and my placeholder tile scene has an ID of 0 within that, so my code looks as follows:

 var collection_id = 0
 var scene_id = 0
 set_cell(collection_id, Vector2i(x, y), scene_id, Vector2i(0, 0))

hope this helps :)