Map Layers issues

OK, So ive had this EXACT same problem and I do have an inkling as I was able to get rid of it in one instance.

Basically the idea has to do with what tiles are surounding the tiles in question, and the visual properties of those tiles. I had the exact same problem with some elements inside of the Figaro Outposts in CoV.

Try copying not only the tiles in question, but also the surrounding tiles by at least 1 in every direction. I found that my graphics clipped through momentarily when I was walking over normal ground before approaching a desk, but when I used the all green carpet tile (not an edge, the actual, totally green one) it wouldn't clip. So grab a bigger chunk around your fence and whittle it down or see what you can edit from there.

Hope this helps! Happy Hacking!