what you see is basically the difference between autotiling on and off.
Intentionally this can be done with shift-click mapping, and is needed for places where you want the effect.
However this should be stored in the mapfile, not in the tileset file.
So there are two different possibilities now:
1) the reconstructed tileset.json is different from the original one and you need to find out where the difference is and correct it.
2) the problem that corrupted the tileset.json also corrupted some maps, and you might have to re-do those maps to correct the effect.
Back home now. I had a good time, but I had a checkup this morning so I had to come home for that. Now I'm just waiting for my therapist meeting tomorrow...
Decided to work on Wishful Wanda today. Since it's a BFB spinoff game, I decided to make the Huang brothers
Easter eggs! I'm actually pitching this to the BFDI team, btw.