Hi there, @mmztech. What are you using for the "Layer/Object Sorting" on your map? With an isometric map you're going to need to use a "Custom Sort Axis". This will also require you to set your Transparency Sort Mode in your Graphics setting as well.
Check this out for further details: https://supertiled2unity.readthedocs.io/en/latest/manual/sorting.html#dynamic-sorting-with-a-custom-sort-axis