That random red dot might be a Layer 1 event left over from the original game. Hit
to enter Layer 1 event editing mode, hold page up to advance all the way through the event list, then drag-select the entire overworld and press delete to remove all the stray tiles.
For the second issue, destruction events are handled through the
dialogue; you have to select a destroyable tile (top of castle/fortress/switch palace) to open it. That said, a destruction event shouldn't run unless the tile Mario is physically on is the tile being destroyed, so I don't know why you'd get an explosion elsewhere.
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