There's nothing of interest in Medina village, just another weird background in the warp room. Similarly, there's nothing interesting in Heckran's cave. There IS something interesting when we return to Truce Canyon, however: we can see the gate key hiding in the top left portion of the screen.

I don't know why it's there, since Lucca doesn't use it at this point, the gate simply opens when you examine it. However, even though the gate key doesn't show up in an animation it will still vanish when you open the time gate.

(NB: It may be the case that the gate key is always here. In fact, in one of the endings when we are shown this screen the key is still hiding in the top left corner. If it IS the case that the key is always there, I didn't see it when I first entered Truce canyon, which is why I mention it here).

Jump forward a ways and we find ourselves in Mystic Mountain, which is the next place where anything significant shows up. Stripping away the top layer of sprites reveals a hidden treasure chest! Unfortunately you can't interact with it, so there's no way of knowing what wonders lie within.

   

What's this scramble? Why, it's a demonstration of what lies beneath the ocean in 6500,0000BC. It's interesting, because this is the only world map to do this. The others simply show blank space when you turn the water off.

This one isn't really a secret since it's something you kinda see while playing the game anyway. Stripping away the top layer of sprites shows the entrance to the cave before Frog uses his sword to blast open the entrance.