You mean when you place something like a coin in the same spot as a ground tile, it cuts off the ground and leaves transparency behind?
Unfortunately, there's no real way around that. All foreground tiles are placed on layer 1, and a layer can only have one tile at a time in the same spot. The SNES can't auto-merge tiles like Mario Maker probably can - in the cases where there are merged tiles (like a ledge corner in front of dirt), they're separate tiles built into SMW.
What you could do is make a layer 2 level, that way, you have both layer 1 and layer 2 available for foreground tiles, and you can place ground on one layer and coins on the other. That also means you have to get rid of the usual background, since layer 2 is normally used for that. If you don't want to make that sacrifice, the easiest thing you can do is create deliberate holes with outlines in the ground, so it doesn't look like the coins cut it off. (Or, even simpler, avoid placing coins on top of ground altogether.)
(Side note: in SMW/Lunar Magic lingo, the word "sprites" refers to enemies and other moving things, not to things placed on the foreground layer. If placing a 1-up creates cutoff, you're probably using the "1-up" checkpoint object by accident, not the 1-up sprite.)