This bizarre blobby background appears in several areas of the game. The texture itself never gets used in the game, it just hides behind other bits of scenery. However, I notice it only appears in areas where you can open up a time gate at some point or another. My theory is that this background is somehow related to the swirling effect that the time gates have.

There are two things that don't agree with this theory, however. First, the background appears when you go to fight Lavos, but it appears orange rather than blue. The time gate in Lavos' lair is blue, just the same as all the others, so why is the background different?

The second part that doesn't add up is the fact that there is a time gate inside Lavos' shell and the background is nowhere to be seen. If the background was related to the time gate effect, surely it would be there.

FO's NOTE: It's been pointed out to me by several different site readers that this background forms the fluctuating outer rim of the time gates. If you look very carefully at the outer circle on the time gates, you should be able to notice that it is actually this background that is visible through it. This is why the time gate that appears inside Lavos's inner shell is the only one in the game that is not animated - because that screen does not have this hidden background.

As for why Lavos's inner shell doesn't have one...I wonder if that time gate was added at the last minute to give you a way out before fighting the final forms of Lavos...maybe they originally wanted you to fight all his forms without being able to save in-between. Or perhaps it's related to the fact that there is no gate if you crash into Lavos with the Epoch. I don't know, so don't quote this as fact.

During the game assorted sprites get hidden under counters for no readily apparent reason. I think this is because of the way the counters are set up. In the above picture, for example, when you talk to the shopkeeper you're not really talking to the shopkeeper, you're talking to the hidden Spekkio sprite. People familiar with the RPG Maker series (especially the XP edition) will be familiar with this practice.

   

Towards the beginning of the game we can find little Spekkio dolls hidden around the map. These dolls are used as event handlers for a variety of purposes, such as indicating which items you have grabbed and whether to show a door as being open or closed. After we beat Yakra, however, this practice abruptly stops and we only see the hidden dolls once or twice for the entirety of the games remainder.
I can think of two possible explanations for this.

The first is that different programming teams worked on different parts of the game, and each team has its own style when it comes to programming event handlers. Perhaps Team A programmed the dungeon underneath the cathedral in a certain way, while Team B programmed Millennial Fair in another.

The second theory is that the game was programmed chronologically. That is, the first thing to get programmed was the intro and Millennial Fair, then Guardia Castle, then the cathedral and so on. If this is the case, the hidden Spekkio dolls may simply serve as an indication of how the games programming evolved during development: eventually surpassing the need to show where event handlers are because the programmers KNOW where they are.

Both of these theories are likely (and, indeed, each is as likely as the other one), so we can only speculate as to why these dolls are hidden where they are.

The island with Geno Dome on it has several craters on it. If we remove these craters we can see one of them turns into a green square. All the other craters disappear when they are removed: this is the only one on the whole of the world map to show as a green square. As such, this is one of the hidden elements I can't even begin to explain. I thought maybe it would be related to Robo's sidequest, but it isn't. So why is it there?

   

There are several places in the game where we can find one layout beneath another. While the two layouts are effectively the same, there are one or two small differences. I believe this is a case of personal preferences on the part of the programmers. In the case shown above, I believe they designed the map with carpeted stairs then redesigned it with stone stairs and kept it that way as a means of looking better.
Why did they keep the old designs in if they put new ones in their place? Probably because nobody would ever see the hidden designs when playing the game on a standard SNES.