Help! How to delete single floor tile?

That roofing that appears inside the house when you fence off that section isn't the roofing above the second floor it's the roofing that extends into the house from that 1 story section on the left side of the house. The game automatically cuts out any portion of roofing that's inside a room that's why it wasn't visible before, but when you add fencing the game for whatever reason designated that room as no longer an interior room (not sure why, but it's a game bug). The simplest fix would be to remove that roof section of the first floor and replace it with a half hipped roof piece that has the flat part against the exterior wall (hope that makes sense xD). It would look exactly the same and you wouldn't have that problem because there would be no roofing inside the house :D

Edit: on a closer inspection it looks like the roofing on the very back of the house is also showing up inside the house. Again remove that full hipped roof section and replace it with a half hipped piece.