Default position for new markers appears to in the middle of the door, which leads to this. As the OP has discovered, you need to move the marker forward of the door and clear of it. Height I've not found to be an issue.
I had this problem with a COC marker at one point for a different reason: I had a gold coin slip under the map at one point. It landed in the void directly under my COC marker, when the game loaded, it forced the coin (Under me) into the map, and then caused both myself and the coin to fall through in this manner.
So, the point: If moving the marker doesn't fix this, make sure you don't have stray items outside the bounds of your map.