@mikimusone Nope. I believe this is a matter of a RetroArch feature which adjusts its cores to run at the Hz expected by the platform running the system. While we usually talk about NTSC games running at 60Hz and PAL games running at 50Hz, we're really generalizing because they actually all run
somewhere in the range of those values and TVs are able to adjust to match the console's refresh rate (within reason). So maybe an NTSC SNES refreshes at a rate point four of a percent faster than a 3DS screen. Instead of skipping .4% of all frames, RetroArch will just slow down the emulated SNES so that it refreshes at the 3DS's rate. It's such a small difference that nobody is likely to notice the change without some kind of external hardware checking the framerate for them.
However, what you're seeing there is that you're running a PAL version game (~50Hz as the message stated) on a ~60Hz screen (the 3DS). This is a huge gap, so RetroArch leaves the emulated refresh rate alone at ~50Hz rather than speeding up the game. You might see a bit of frame juddering because the 3DS still has to display 60 frames per second but the core is only providing 50, so 10 of those 50 frames will just have to display twice.
On the subject of Terranigma, I'd recommend applying
this patch which adjusts the ROM header to specify that it's a US cart and patches out the region lock. It means the game will run at 60Hz and this will look much better on the 3DS (and play at the intended gameplay speed, as the PAL release wasn't optimized to account for the 50/60Hz difference). There's essentially no reason to play the game at 50Hz. Incidentally, this game seems to work pretty well on blargSNES. I only tried it for a couple of minutes, but unless it breaks later, you'd be better off there instead of RetroArch.
For clarity, there's no setting you can change to fix the current scaling behavior in RetroArch 3DS. That's just a result of it being very early software that's not fully functional yet.