If you run into a godot error like I did for the tileset. it will look like this:
0:00:00:0925 create_tile: Cannot create tile. The tile is outside the texture or tiles are already present in the space the tile would cover.
E 0:00:00:0925 has_alternative_tile: The TileSetAtlasSource atlas has no tile at (0, 6).
After testing 1 by 1 the issues is "Waterfall - c1"
Manually removing and re-adding and manually creating the animation atlas fixes this issue.
The waterfall - c1 provides 9 errors, but as it is duplicated on the other tileset it generates 18 total.