I also think/hope I might have fixed the issue of single tiles having weird city borders, as if they are settlements of their own. The game sometimes thinks a tile which was aquired in a settlement, already had a previous owner (no idea why), but then couldn't find the tile in the owned-by-someone list and created a new entry in that list for the non-existing previous owner, resulting in a tile that looks like it is a settlement on its own. I suppress that creation to avoid the game confusing itself.
I now do know what happens. Tiles with discoveries (goody huts) have a special kind of owner internally, as if all the goody huts combined form an empire of their own. When the discovery is cleared by a player, the "Goody Hut Empire" ownership is not completely removed from that tile. When a settlement later expands into that tile, the game finds that the tile has a previous owner, but cannot determine what the owner is and often creates a new border for that single tile, as if it is a settlement on its own. Now it's a mini-empire of sorts. It keeps this status until a reload, at which time the border is calculated from scratch which is much more error-proof.
This is visible in the UI.log when using the 4.0 beta-3 version.
The civ border is calculated completely independent from the city border and does not have this issue.
The 4.0 beta version seems to solve this issue correctly. I'll do some more testing myself and await feedback before publishing a real 4.0 version.